# Graph Report - .  (2026-05-07)

## Corpus Check
- 0 files · ~0 words
- Verdict: corpus is large enough that graph structure adds value.

## Summary
- 12917 nodes · 18952 edges · 1050 communities (531 shown, 519 thin omitted)
- Extraction: 73% EXTRACTED · 27% INFERRED · 0% AMBIGUOUS · INFERRED: 5063 edges (avg confidence: 0.68)
- Token cost: 0 input · 0 output

## Community Hubs (Navigation)
- [[_COMMUNITY_Test Fixtures & Process Utilities|Test Fixtures & Process Utilities]]
- [[_COMMUNITY_Result Serialization & Messaging|Result Serialization & Messaging]]
- [[_COMMUNITY_JAX Backend & Config Toggles|JAX Backend & Config Toggles]]
- [[_COMMUNITY_CMC Priors & Sampler Core|CMC Priors & Sampler Core]]
- [[_COMMUNITY_Optimization Enums & Logging|Optimization Enums & Logging]]
- [[_COMMUNITY_Checkpoint & Resume System|Checkpoint & Resume System]]
- [[_COMMUNITY_CMC Config & Runner|CMC Config & Runner]]
- [[_COMMUNITY_NLSQ Memory & Strategy Tests|NLSQ Memory & Strategy Tests]]
- [[_COMMUNITY_MCMC Diagnostics & Monitoring|MCMC Diagnostics & Monitoring]]
- [[_COMMUNITY_Gradient & Regularizer Tests|Gradient & Regularizer Tests]]
- [[_COMMUNITY_Data Structures & Base Classes|Data Structures & Base Classes]]
- [[_COMMUNITY_Per-Angle Scaling Modes|Per-Angle Scaling Modes]]
- [[_COMMUNITY_CMC Backend & Bimodal Detection|CMC Backend & Bimodal Detection]]
- [[_COMMUNITY_CMC Result & Sampling Plan|CMC Result & Sampling Plan]]
- [[_COMMUNITY_JAX JIT  vmap Primitives|JAX JIT / vmap Primitives]]
- [[_COMMUNITY_NLSQ Multi-Start & Bounds|NLSQ Multi-Start & Bounds]]
- [[_COMMUNITY_Test Mock Fixtures|Test Mock Fixtures]]
- [[_COMMUNITY_NLSQ Config & CMA-ES|NLSQ Config & CMA-ES]]
- [[_COMMUNITY_CMC Data Prep & Sharding|CMC Data Prep & Sharding]]
- [[_COMMUNITY_Config Manager & YAML|Config Manager & YAML]]
- [[_COMMUNITY_.Fit()  Adapter.Py|.Fit() / Adapter.Py]]
- [[_COMMUNITY_Weighter()  .  Init  ()|Weighter() / .  Init  ()]]
- [[_COMMUNITY_.Copy()  .  Str  ()|.Copy() / .  Str  ()]]
- [[_COMMUNITY_Test Streaming Optimizer.Py  Test Confi|Test Streaming Optimizer.Py / Test Confi]]
- [[_COMMUNITY_.  Init  ()  .Get Bounds()|.  Init  () / .Get Bounds()]]
- [[_COMMUNITY_Jit()  Grad()|Jit() / Grad()]]
- [[_COMMUNITY_From Config()  From Defaults()|From Config() / From Defaults()]]
- [[_COMMUNITY_.Run()  Main()|.Run() / Main()]]
- [[_COMMUNITY_User Guide Index  Xpcsdataloader Class|User Guide Index / Xpcsdataloader Class]]
- [[_COMMUNITY_Valid Data()  Mock Loader()|Valid Data() / Mock Loader()]]
- [[_COMMUNITY_Jit()  Vmap()|Jit() / Vmap()]]
- [[_COMMUNITY_.  Init  ()  Testcaching|.  Init  () / Testcaching]]
- [[_COMMUNITY_Dict  .Fit()|Dict / .Fit()]]
- [[_COMMUNITY_Json Safe()  Testjsonsafe|Json Safe() / Testjsonsafe]]
- [[_COMMUNITY_Testanglevalidation  Testoptimizationed|Testanglevalidation / Testoptimizationed]]
- [[_COMMUNITY_Get Docs Path()  Testanalysismodes|Get Docs Path() / Testanalysismodes]]
- [[_COMMUNITY_Get Docs Path()  Testcodeexamples|Get Docs Path() / Testcodeexamples]]
- [[_COMMUNITY_Bounddict  Testbounddicttype|Bounddict / Testbounddicttype]]
- [[_COMMUNITY_Mockchunk  .  Call  ()|Mockchunk / .  Call  ()]]
- [[_COMMUNITY_Log Calls()  Log Phase()|Log Calls() / Log Phase()]]
- [[_COMMUNITY_Testcoordinateaxes  Test Data Loader.Py|Testcoordinateaxes / Test Data Loader.Py]]
- [[_COMMUNITY_Testnlsqfallback  Test Nlsq Core.Py|Testnlsqfallback / Test Nlsq Core.Py]]
- [[_COMMUNITY_Io.Py  Test Io.Py|Io.Py / Test Io.Py]]
- [[_COMMUNITY_Jit()  Grad()|Jit() / Grad()]]
- [[_COMMUNITY_.Test Str()  .Test Repr()|.Test Str() / .Test Repr()]]
- [[_COMMUNITY_Combinedmodel  Model Static()|Combinedmodel / Model Static()]]
- [[_COMMUNITY_. Make Config With Cmc()  Num Warmup=0|. Make Config With Cmc() / Num Warmup=0 ]]
- [[_COMMUNITY_Gradientresult  Numpy Hessian()|Gradientresult / Numpy Hessian()]]
- [[_COMMUNITY_Async Io.Py  Asyncwriter|Async Io.Py / Asyncwriter]]
- [[_COMMUNITY_Nlsqresult  .  Init  ()|Nlsqresult / .  Init  ()]]
- [[_COMMUNITY_.Test Boundary Tolerance()  .Test Multi|.Test Boundary Tolerance() / .Test Multi]]
- [[_COMMUNITY_Anglesubset  Simple Dataset()|Anglesubset / Simple Dataset()]]
- [[_COMMUNITY_Testconfiggeneratorparser  .Test Parser|Testconfiggeneratorparser / .Test Parser]]
- [[_COMMUNITY_Protocol  .Compute G2()|Protocol / .Compute G2()]]
- [[_COMMUNITY_Config.Py  Get Logger()|Config.Py / Get Logger()]]
- [[_COMMUNITY_Model Func()  Testjitcompilation|Model Func() / Testjitcompilation]]
- [[_COMMUNITY_Testparamcountbymode  Testgetmodelparam|Testparamcountbymode / Testgetmodelparam]]
- [[_COMMUNITY_Model()  Models.Py|Model() / Models.Py]]
- [[_COMMUNITY_.Run()  Pbs.Py|.Run() / Pbs.Py]]
- [[_COMMUNITY_Reparamconfig  Testreparamconfig|Reparamconfig / Testreparamconfig]]
- [[_COMMUNITY_.  New  ()  Get Bounds()|.  New  () / Get Bounds()]]
- [[_COMMUNITY_Types.Py  Cmcconfig|Types.Py / Cmcconfig]]
- [[_COMMUNITY_.Fit()  .Check()|.Fit() / .Check()]]
- [[_COMMUNITY_Save Nlsq Results()  Testcomputenlsqfit|Save Nlsq Results() / Testcomputenlsqfit]]
- [[_COMMUNITY_Jit()    Init  ()|Jit() /   Init  ()]]
- [[_COMMUNITY_.Run()  Pjit.Py|.Run() / Pjit.Py]]
- [[_COMMUNITY_Is Linux()  Is Macos()|Is Linux() / Is Macos()]]
- [[_COMMUNITY_Full Params()  Shear Params()|Full Params() / Shear Params()]]
- [[_COMMUNITY_Main()  .Log()|Main() / .Log()]]
- [[_COMMUNITY_.  Init  ()  .End Phase()|.  Init  () / .End Phase()]]
- [[_COMMUNITY_Synthetic C2 Data()  Testnlsqperformanc|Synthetic C2 Data() / Testnlsqperformanc]]
- [[_COMMUNITY_Testmalformedconfigfiles  Test Config V|Testmalformedconfigfiles / Test Config V]]
- [[_COMMUNITY_Sequential.Py   Jax Jacobian()|Sequential.Py /  Jax Jacobian()]]
- [[_COMMUNITY_Parser()  Mock Config()|Parser() / Mock Config()]]
- [[_COMMUNITY_.With Info()  Resultbuilder|.With Info() / Resultbuilder]]
- [[_COMMUNITY_.  Call  ()  .  Init  ()|.  Call  () / .  Init  ()]]
- [[_COMMUNITY_Test Get Diagnostics()  Test Stratified|Test Get Diagnostics() / Test Stratified]]
- [[_COMMUNITY_Testapplyanglefiltering   Apply Angle F|Testapplyanglefiltering /  Apply Angle F]]
- [[_COMMUNITY_Testnlsqwrapperfit  .Test Fit Logs Iter|Testnlsqwrapperfit / .Test Fit Logs Iter]]
- [[_COMMUNITY_Safe Len()  Testsafelen|Safe Len() / Testsafelen]]
- [[_COMMUNITY_Tmp Hdf5 Dir()  Synthetic Hdf5()|Tmp Hdf5 Dir() / Synthetic Hdf5()]]
- [[_COMMUNITY_Test Config Error Paths.Py  Testconfigv|Test Config Error Paths.Py / Testconfigv]]
- [[_COMMUNITY_Data Prep.Py  Validate Bounds()|Data Prep.Py / Validate Bounds()]]
- [[_COMMUNITY_Valueerror  .To Fourier()|Valueerror / .To Fourier()]]
- [[_COMMUNITY_Mockchunk  Mockchunkeddata|Mockchunk / Mockchunkeddata]]
- [[_COMMUNITY_.Test Symmetry()  .Test Non Negative()|.Test Symmetry() / .Test Non Negative()]]
- [[_COMMUNITY_.Cleanup()  .  Init  ()|.Cleanup() / .  Init  ()]]
- [[_COMMUNITY_Testnlsqconfigvalidation  .Test Invalid|Testnlsqconfigvalidation / .Test Invalid]]
- [[_COMMUNITY_Jit()  Grad()|Jit() / Grad()]]
- [[_COMMUNITY_.Close()  .Close()|.Close() / .Close()]]
- [[_COMMUNITY_.To Dict()  From Dict()|.To Dict() / From Dict()]]
- [[_COMMUNITY_Testvalidatesavepath  Validate Save Pat|Testvalidatesavepath / Validate Save Pat]]
- [[_COMMUNITY_Plot Ess()   Plot Rhat()| Plot Ess() /  Plot Rhat()]]
- [[_COMMUNITY_Testphysicsconstraints   Compute C2 Mod|Testphysicsconstraints /  Compute C2 Mod]]
- [[_COMMUNITY_.Test Zero D0()  .Test Positive Output(|.Test Zero D0() / .Test Positive Output(]]
- [[_COMMUNITY_Safe Sinc()  Testsafesinc|Safe Sinc() / Testsafesinc]]
- [[_COMMUNITY_Testdtpropagation  Testtimegridgenerati|Testdtpropagation / Testtimegridgenerati]]
- [[_COMMUNITY_Tmp Output Dir()  Testcliinvalidconfig|Tmp Output Dir() / Testcliinvalidconfig]]
- [[_COMMUNITY_Theory.Py  .  Init  ()|Theory.Py / .  Init  ()]]
- [[_COMMUNITY_.Fit()  Is Available()|.Fit() / Is Available()]]
- [[_COMMUNITY_Compute G1()  Compute G1 Shear()|Compute G1() / Compute G1 Shear()]]
- [[_COMMUNITY_Main()  Set Mode()|Main() / Set Mode()]]
- [[_COMMUNITY_Logging.Py  .Process()|Logging.Py / .Process()]]
- [[_COMMUNITY_Get Venv Path()  Post Install.Py|Get Venv Path() / Post Install.Py]]
- [[_COMMUNITY_.  Str  ()  Test Physics.Py|.  Str  () / Test Physics.Py]]
- [[_COMMUNITY_.  Repr  ()  .Is Parameter Active()|.  Repr  () / .Is Parameter Active()]]
- [[_COMMUNITY_Message()  .Tolist()|Message() / .Tolist()]]
- [[_COMMUNITY_Path Validation.Py  Testsanitizelogpath|Path Validation.Py / Testsanitizelogpath]]
- [[_COMMUNITY_Testtoworkflowkwargsvalid  Random Sampl|Testtoworkflowkwargsvalid / Random Sampl]]
- [[_COMMUNITY_Testcompletionaliases  .Test Aliases Pr|Testcompletionaliases / .Test Aliases Pr]]
- [[_COMMUNITY_Testnaninfinjection  .Test Inf In Loss(|Testnaninfinjection / .Test Inf In Loss(]]
- [[_COMMUNITY_Testanglenormalization  Test Angle Filt|Testanglenormalization / Test Angle Filt]]
- [[_COMMUNITY_Mock Data()  Mock Result()|Mock Data() / Mock Result()]]
- [[_COMMUNITY_Compute T Ref()  Testcomputetref|Compute T Ref() / Testcomputetref]]
- [[_COMMUNITY_.  Exit  ()  .Shutdown()|.  Exit  () / .Shutdown()]]
- [[_COMMUNITY_.Test Import()  .Test No Data Loss()|.Test Import() / .Test No Data Loss()]]
- [[_COMMUNITY_Recovery.Py  Diagnose Error()|Recovery.Py / Diagnose Error()]]
- [[_COMMUNITY_Array To Params()   Params To Array()| Array To Params() /  Params To Array()]]
- [[_COMMUNITY_Test Nlsq Ooc Routing.Py  Testoutofcore|Test Nlsq Ooc Routing.Py / Testoutofcore]]
- [[_COMMUNITY_Testoptimizationstrategy  .Test Strateg|Testoptimizationstrategy / .Test Strateg]]
- [[_COMMUNITY_Logconfiguration  Worker Function()|Logconfiguration / Worker Function()]]
- [[_COMMUNITY_Jit()   Is Jax Array()|Jit() /  Is Jax Array()]]
- [[_COMMUNITY_Rng()  Simple Matrix()|Rng() / Simple Matrix()]]
- [[_COMMUNITY_.Test Get Prior Means()  .Test Get Boun|.Test Get Prior Means() / .Test Get Boun]]
- [[_COMMUNITY_Testbetascaledintegration  Static Confi|Testbetascaledintegration / Static Confi]]
- [[_COMMUNITY_.Test Diagnostics()  .Test Reset Monito|.Test Diagnostics() / .Test Reset Monito]]
- [[_COMMUNITY_Apply Cli Overrides()  Test Overriding| Apply Cli Overrides() / Test Overriding]]
- [[_COMMUNITY_.Test Valid Eps Path()  .Test Valid Pdf|.Test Valid Eps Path() / .Test Valid Pdf]]
- [[_COMMUNITY_Testjaxgradientflow  Testjaxfancyindexi|Testjaxgradientflow / Testjaxfancyindexi]]
- [[_COMMUNITY_.  Call  ()   Get Param Names()|.  Call  () /  Get Param Names()]]
- [[_COMMUNITY_Test Sphinx Rst Formatting()  Test Conf|Test Sphinx Rst Formatting() / Test Conf]]
- [[_COMMUNITY_Temp Dir()  Xpcs Config()|Temp Dir() / Xpcs Config()]]
- [[_COMMUNITY_Datasetmetadata  .Create 1B Dataset()|Datasetmetadata / .Create 1B Dataset()]]
- [[_COMMUNITY_Main()  .To Dict()|Main() / .To Dict()]]
- [[_COMMUNITY_Physics.Py  Parameter Bounds()|Physics.Py / Parameter Bounds()]]
- [[_COMMUNITY_Init  .Py  Get Device Status()|  Init  .Py / Get Device Status()]]
- [[_COMMUNITY_Time Grid()  Phi Angles()|Time Grid() / Phi Angles()]]
- [[_COMMUNITY_Get Xpcs Model()  Testmodelselection|Get Xpcs Model() / Testmodelselection]]
- [[_COMMUNITY_Testdatavalidationedgecases  .Test Vali|Testdatavalidationedgecases / .Test Vali]]
- [[_COMMUNITY_Testcorrelationdata  .Test C2 Maximum V|Testcorrelationdata / .Test C2 Maximum V]]
- [[_COMMUNITY_.Format()  Constraintrule|.Format() / Constraintrule]]
- [[_COMMUNITY_Testangleinrange   Angle In Range()|Testangleinrange /  Angle In Range()]]
- [[_COMMUNITY_.Test Value And Grad()  .Test Forward M|.Test Value And Grad() / .Test Forward M]]
- [[_COMMUNITY_.Test Linear Shear()  Calculate Shear R|.Test Linear Shear() / Calculate Shear R]]
- [[_COMMUNITY_Validate Args()  Testcliparameteroverri|Validate Args() / Testcliparameteroverri]]
- [[_COMMUNITY_.Test Case Insensitive()  Normalize Ana|.Test Case Insensitive() / Normalize Ana]]
- [[_COMMUNITY_Test Nlsq Saving.Py  Testsavenlsqnpzfil|Test Nlsq Saving.Py / Testsavenlsqnpzfil]]
- [[_COMMUNITY_Testoptimizationresult  .Test Result Ha|Testoptimizationresult / .Test Result Ha]]
- [[_COMMUNITY_Testnlsqconfigfromdict  .Test From Empt|Testnlsqconfigfromdict / .Test From Empt]]
- [[_COMMUNITY_Config.Py  Hardwareconfig|Config.Py / Hardwareconfig]]
- [[_COMMUNITY_Model.Py  Xpcs Model Averaged()|Model.Py / Xpcs Model Averaged()]]
- [[_COMMUNITY_Init  .Py  Api Cmc Module|  Init  .Py / Api: Cmc Module]]
- [[_COMMUNITY_Samplingplan  Reparamconfig|Samplingplan / Reparamconfig]]
- [[_COMMUNITY_Main()  Namedtuple|Main() / Namedtuple]]
- [[_COMMUNITY_Performance Benchmarks  .Test Vmap Corr|Performance Benchmarks / .Test Vmap Corr]]
- [[_COMMUNITY_.  Init  ()  .Get Prior()|.  Init  () / .Get Prior()]]
- [[_COMMUNITY_Physics Params()  Testcmcphysicsvalues|Physics Params() / Testcmcphysicsvalues]]
- [[_COMMUNITY_Load Data()  Testdataloading| Load Data() / Testdataloading]]
- [[_COMMUNITY_Mock Parameter Space()  .Test Bounds Cl|Mock Parameter Space() / .Test Bounds Cl]]
- [[_COMMUNITY_Testdatavalidation  Test Sigma Is Posit|Testdatavalidation / Test Sigma Is Posit]]
- [[_COMMUNITY_Validate Experimental Setup()  .Test Va|Validate Experimental Setup() / .Test Va]]
- [[_COMMUNITY_Get Num Parameters()  Get Parameter Nam|Get Num Parameters() / Get Parameter Nam]]
- [[_COMMUNITY_Main()  Nlsqdata|Main() / Nlsqdata]]
- [[_COMMUNITY_Infer Time Step()  Testcmctimestepinfe| Infer Time Step() / Testcmctimestepinfe]]
- [[_COMMUNITY_Fit Mcmc Jax()  Multi Angle Data()|Fit Mcmc Jax() / Multi Angle Data()]]
- [[_COMMUNITY_.Test Diagnostics()  .Test Reset Clears|.Test Diagnostics() / .Test Reset Clears]]
- [[_COMMUNITY_Plot Ess()  Plot Pair()|Plot Ess() / Plot Pair()]]
- [[_COMMUNITY_Testgetsafeoutputdir  Get Safe Output D|Testgetsafeoutputdir / Get Safe Output D]]
- [[_COMMUNITY_Testcpudetection  Benchmark Cpu Perform|Testcpudetection / Benchmark Cpu Perform]]
- [[_COMMUNITY_Safe Exp()  Testsafeexp|Safe Exp() / Testsafeexp]]
- [[_COMMUNITY_Normalize Nlsq Result()  Testnormalizen|Normalize Nlsq Result() / Testnormalizen]]
- [[_COMMUNITY_.Test Single Angle Range()  Testanglefi|.Test Single Angle Range() / Testanglefi]]
- [[_COMMUNITY_Testnlsqconfigconstantscaling  .Test Co|Testnlsqconfigconstantscaling / .Test Co]]
- [[_COMMUNITY_Test Project Metadata()  Test Warning S|Test Project Metadata() / Test Warning S]]
- [[_COMMUNITY_Core.Py   Fmt Time()|Core.Py /  Fmt Time()]]
- [[_COMMUNITY_Physics Nlsq.Py  Compute G2 Scaled()|Physics Nlsq.Py / Compute G2 Scaled()]]
- [[_COMMUNITY_Shardgrid  Physics Cmc.Py|Shardgrid / Physics Cmc.Py]]
- [[_COMMUNITY_Testmodelphysics  Xpcs Model Scaled()|Testmodelphysics / Xpcs Model Scaled()]]
- [[_COMMUNITY_.Test Both Transforms()  .Test D Ref Tr|.Test Both Transforms() / .Test D Ref Tr]]
- [[_COMMUNITY_Api Jax Backend  Data Handler Architec|Api: Jax Backend / Data Handler Architec]]
- [[_COMMUNITY_Test Uninstall.Py  Testremovehomodynebl|Test Uninstall.Py / Testremovehomodynebl]]
- [[_COMMUNITY_.Test Output Shape()  .Test Small Matri|.Test Output Shape() / .Test Small Matri]]
- [[_COMMUNITY_Test Config Manager.Py  Testparameterna|Test Config Manager.Py / Testparameterna]]
- [[_COMMUNITY_.Test Beta Out Of Range()  .Test Negati|.Test Beta Out Of Range() / .Test Negati]]
- [[_COMMUNITY_Testworkerpool  .Test Worker Reuse()|Testworkerpool / .Test Worker Reuse()]]
- [[_COMMUNITY_.Test Single Chunk()  .Test Identical R|.Test Single Chunk() / .Test Identical R]]
- [[_COMMUNITY_Nlsq Plots.Py  Generate Nlsq Plots()|Nlsq Plots.Py / Generate Nlsq Plots()]]
- [[_COMMUNITY_Commands.Py   Save Results()|Commands.Py /  Save Results()]]
- [[_COMMUNITY_Log Exception()  Testlogexception|Log Exception() / Testlogexception]]
- [[_COMMUNITY_Test Api Documentation.Py  Test Core Mo|Test Api Documentation.Py / Test Core Mo]]
- [[_COMMUNITY_Standardexecutor  Teststandardexecutor|Standardexecutor / Teststandardexecutor]]
- [[_COMMUNITY_Get Executor()  Testgetexecutor|Get Executor() / Testgetexecutor]]
- [[_COMMUNITY_Testjaxarraycreation  .Test Meshgrid Cr|Testjaxarraycreation / .Test Meshgrid Cr]]
- [[_COMMUNITY_Testparameterboundsdetection   Classify|Testparameterboundsdetection /  Classify]]
- [[_COMMUNITY_Abc  Fit()|Abc / Fit()]]
- [[_COMMUNITY_Testvalidateinput  Nan In T1 Raises Val|Testvalidateinput / Nan In T1 Raises Val]]
- [[_COMMUNITY_Testnlsqwrapperinit  .Test Wrapper Init|Testnlsqwrapperinit / .Test Wrapper Init]]
- [[_COMMUNITY_Testconsistentperangleinit  . Create Mo|Testconsistentperangleinit / . Create Mo]]
- [[_COMMUNITY_Testnlsqconfigdefaults  .Test Default L|Testnlsqconfigdefaults / .Test Default L]]
- [[_COMMUNITY_Testcmcconfigperanglemode  .Test Defaul|Testcmcconfigperanglemode / .Test Defaul]]
- [[_COMMUNITY_.Test Inf In C2()  .Test Nan In C2()|.Test Inf In C2() / .Test Nan In C2()]]
- [[_COMMUNITY_Enable D Total()  Enable Log Gamma()|Enable D Total() / Enable Log Gamma()]]
- [[_COMMUNITY_Testcmcresult  .Test Ess Values()|Testcmcresult / .Test Ess Values()]]
- [[_COMMUNITY_Testcmcresultvalidation  .Test Validate|Testcmcresultvalidation / .Test Validate]]
- [[_COMMUNITY_Testcmcconfig  .Test Default Values()|Testcmcconfig / .Test Default Values()]]
- [[_COMMUNITY_Get Template Path()  Testgettemplatepat|Get Template Path() / Testgettemplatepat]]
- [[_COMMUNITY_.Test From Dict()  Testlogconfiguration|.Test From Dict() / Testlogconfiguration]]
- [[_COMMUNITY_Test Logging.Py  Testwithcontextshard|Test Logging.Py / Testwithcontextshard]]
- [[_COMMUNITY_.Submit()  Workerpool|.Submit() / Workerpool]]
- [[_COMMUNITY_Fallback Chain.Py   Get Strategy Info()|Fallback Chain.Py /  Get Strategy Info()]]
- [[_COMMUNITY_Main()  Print Usage Guide()|Main() / Print Usage Guide()]]
- [[_COMMUNITY_Main()  Cpu Optimization.Py|Main() / Cpu Optimization.Py]]
- [[_COMMUNITY_Name()  Execute()|Name() / Execute()]]
- [[_COMMUNITY_.  Init  ()  .Snapshot()|.  Init  () / .Snapshot()]]
- [[_COMMUNITY_.Apply()  .Format()|.Apply() / .Format()]]
- [[_COMMUNITY_Shearmodel  Diffusionmodel|Shearmodel / Diffusionmodel]]
- [[_COMMUNITY_.Test Zeros Matrix()  .Test Uniform Val|.Test Zeros Matrix() / .Test Uniform Val]]
- [[_COMMUNITY_Testconfigloadingedgecases  .Test Load|Testconfigloadingedgecases / .Test Load ]]
- [[_COMMUNITY_Testparameterexpansion  .Test Bounds Ex|Testparameterexpansion / .Test Bounds Ex]]
- [[_COMMUNITY_Test With Infinity Values.  Testinvalid|Test With Infinity Values. / Testinvalid]]
- [[_COMMUNITY_Testparameterspacefromconfig  .Test Loa|Testparameterspacefromconfig / .Test Loa]]
- [[_COMMUNITY_.Test Static Params Count()  .Test Scal|.Test Static Params Count() / .Test Scal]]
- [[_COMMUNITY_Test Error For D0 = 0.  .Test Multiple|Test Error For D0 = 0. / .Test Multiple ]]
- [[_COMMUNITY_Testt0Exclusion   Exclude T0 From Analy|Testt0Exclusion /  Exclude T0 From Analy]]
- [[_COMMUNITY_.  Init  ()  Inputvalidator|.  Init  () / Inputvalidator]]
- [[_COMMUNITY_.Validate All()  Input Validator.Py|.Validate All() / Input Validator.Py]]
- [[_COMMUNITY_.  Repr  ()  Homodynemodel|.  Repr  () / Homodynemodel]]
- [[_COMMUNITY_Trapezoid Cumsum()  Testtrapezoidcumsum|Trapezoid Cumsum() / Testtrapezoidcumsum]]
- [[_COMMUNITY_Testmethodargumentparsing  .Test Method|Testmethodargumentparsing / .Test Method]]
- [[_COMMUNITY_.Test Good Quality Fit()  .Test Poor Qu|.Test Good Quality Fit() / .Test Poor Qu]]
- [[_COMMUNITY_Testnlsqadapterbase  .Test Adapter Base|Testnlsqadapterbase / .Test Adapter Base]]
- [[_COMMUNITY_.Test Wavevector T1 T2 Unchanged()  .Te|.Test Wavevector T1 T2 Unchanged() / .Te]]
- [[_COMMUNITY_Testnlsqconfigtodict  .Test To Dict Rou|Testnlsqconfigtodict / .Test To Dict Rou]]
- [[_COMMUNITY_Parameterscaling  Testparameterscaling|Parameterscaling / Testparameterscaling]]
- [[_COMMUNITY_.  Init  ()  .Get Prior()|.  Init  () / .Get Prior()]]
- [[_COMMUNITY_Mock Parameter Space()  .Test Transform|Mock Parameter Space() / .Test Transform]]
- [[_COMMUNITY_Testvalidateplotarrays  .Test Names Opt|Testvalidateplotarrays / .Test Names Opt]]
- [[_COMMUNITY_.Test All Inf Array()  Test Viz Validat|.Test All Inf Array() / Test Viz Validat]]
- [[_COMMUNITY_Configmanager  Homodynemodel|Configmanager / Homodynemodel]]
- [[_COMMUNITY_Configuration Index  Configure Cpu Hpc(|Configuration Index / Configure Cpu Hpc(]]
- [[_COMMUNITY_Test Workflows.Py  Testendtoendworkflow|Test Workflows.Py / Testendtoendworkflow]]
- [[_COMMUNITY_.  Init  ()  Resultvalidator|.  Init  () / Resultvalidator]]
- [[_COMMUNITY_Nlsqadapter  Nlsqwrapper|Nlsqadapter / Nlsqwrapper]]
- [[_COMMUNITY_Testhdf5Formatdetection  .Create Mock A|Testhdf5Formatdetection / .Create Mock A]]
- [[_COMMUNITY_Clip Parameters()  Testclipparametersed|Clip Parameters() / Testclipparametersed]]
- [[_COMMUNITY_Testcombinedmodeledgecases  .Test Compu|Testcombinedmodeledgecases / .Test Compu]]
- [[_COMMUNITY_Validate Parameter Names()  Testparamet|Validate Parameter Names() / Testparamet]]
- [[_COMMUNITY_Testparameterbounds  .Test Get Bounds A|Testparameterbounds / .Test Get Bounds A]]
- [[_COMMUNITY_.Test All Active()  .Test At Lower Boun|.Test All Active() / .Test At Lower Boun]]
- [[_COMMUNITY_Testadaptivechunksize  .Test No Angles|Testadaptivechunksize / .Test No Angles ]]
- [[_COMMUNITY_Ooc Worker Init()  Create Ooc Kernels(| Ooc Worker Init() / Create Ooc Kernels(]]
- [[_COMMUNITY_.  Init  ()  . Get Colormap()|.  Init  () / . Get Colormap()]]
- [[_COMMUNITY_Validate Covariance()  Testvalidatecova|Validate Covariance() / Testvalidatecova]]
- [[_COMMUNITY_.Validate All()  Nan Chi-Squared Fails.|.Validate All() / Nan Chi-Squared Fails.]]
- [[_COMMUNITY_Finite Parameters Pass.  .Test Inf Para|Finite Parameters Pass. / .Test Inf Para]]
- [[_COMMUNITY_Testcmcargumentparsing  .Test Cmc Backe|Testcmcargumentparsing / .Test Cmc Backe]]
- [[_COMMUNITY_Optimization Runner.Py   Run Nlsq Optim|Optimization Runner.Py /  Run Nlsq Optim]]
- [[_COMMUNITY_Plot Dispatch.Py   Handle Plotting()|Plot Dispatch.Py /  Handle Plotting()]]
- [[_COMMUNITY_Config.Py  From Dict()|Config.Py / From Dict()]]
- [[_COMMUNITY_Testlhsgeneration  Generate Lhs Starts(|Testlhsgeneration / Generate Lhs Starts(]]
- [[_COMMUNITY_.Test Compute C2 Shape()  .Test Compute|.Test Compute C2 Shape() / .Test Compute]]
- [[_COMMUNITY_.  Str  ()  .To Dict()|.  Str  () / .To Dict()]]
- [[_COMMUNITY_Testjaxcompilationexpanded  .Test Jit F|Testjaxcompilationexpanded / .Test Jit F]]
- [[_COMMUNITY_Testmeshgridcache  Reset Cache Stats()|Testmeshgridcache / Reset Cache Stats()]]
- [[_COMMUNITY_.Test Success False Failed()  Determine|.Test Success False Failed() / Determine]]
- [[_COMMUNITY_Result Saving.Py  Save Mcmc Results()|Result Saving.Py / Save Mcmc Results()]]
- [[_COMMUNITY_.As Dict()   Json Safe()|.As Dict() /  Json Safe()]]
- [[_COMMUNITY_.Test Batch Statistics Export()  .Test|.Test Batch Statistics Export() / .Test ]]
- [[_COMMUNITY_Config Factory.Py  Create Empty Ranges|Config Factory.Py / Create Empty Ranges ]]
- [[_COMMUNITY_.Stop()  .Start()|.Stop() / .Start()]]
- [[_COMMUNITY_Teststage7Nlsqpriorsconfig  .Test Defau|Teststage7Nlsqpriorsconfig / .Test Defau]]
- [[_COMMUNITY_Main()  Create Parser()|Main() / Create Parser()]]
- [[_COMMUNITY_Testlogphase  .Test Custom Logger()|Testlogphase / .Test Custom Logger()]]
- [[_COMMUNITY_Main()  Count Dir()|Main() / Count Dir()]]
- [[_COMMUNITY_Andrade Creep Law Gamma ~ T(13)  Tayl|Andrade Creep Law Gamma ~ T^(1/3) / Tayl]]
- [[_COMMUNITY_Teststage3Shardsize   Resolve Max Point|Teststage3Shardsize /  Resolve Max Point]]
- [[_COMMUNITY_Cpu.Py  Configure Cpu Hpc()|Cpu.Py / Configure Cpu Hpc()]]
- [[_COMMUNITY_Hit Rate()  Log Calls()|Hit Rate() / Log Calls()]]
- [[_COMMUNITY_Memorypool  .Get Buffer()|Memorypool / .Get Buffer()]]
- [[_COMMUNITY_Residual.Py  .Get Diagnostics()|Residual.Py / .Get Diagnostics()]]
- [[_COMMUNITY_Sample Xdata()  Parameter Utils.Py|Sample Xdata() / Parameter Utils.Py]]
- [[_COMMUNITY_.To Dict()  Fit Quality.Py|.To Dict() / Fit Quality.Py]]
- [[_COMMUNITY_Testnlsqoptimizationmemory  .Test Jacob|Testnlsqoptimizationmemory / .Test Jacob]]
- [[_COMMUNITY_Configfactory  Data Factory.Py|Configfactory / Data Factory.Py]]
- [[_COMMUNITY_Test Config Generator.Py  Testfallbacky|Test Config Generator.Py / Testfallbacky]]
- [[_COMMUNITY_Shearmodel (4 Params)  Physics Models A|Shearmodel (4 Params) / Physics Models A]]
- [[_COMMUNITY_Adr-005 Per-Angle Scaling Modes  Five-|Adr-005: Per-Angle Scaling Modes / Five-]]
- [[_COMMUNITY_Troubleshooting Guide  Frequently Asked|Troubleshooting Guide / Frequently Asked]]
- [[_COMMUNITY_Testunifiedmoduleapi  Get Available Bac|Testunifiedmoduleapi / Get Available Bac]]
- [[_COMMUNITY_Testbatchprocessing  .Test Batch Numpy|Testbatchprocessing / .Test Batch Numpy ]]
- [[_COMMUNITY_.Test Basic Method()  Testunifiedmodule|.Test Basic Method() / Testunifiedmodule]]
- [[_COMMUNITY_Testdiagonalcorrectionbasic  .Test Off|Testdiagonalcorrectionbasic / .Test Off ]]
- [[_COMMUNITY_Phi Filtering.Py  Filter Phi Angles()|Phi Filtering.Py / Filter Phi Angles()]]
- [[_COMMUNITY_Testdiffusionmodeledgecases  .Test Comp|Testdiffusionmodeledgecases / .Test Comp]]
- [[_COMMUNITY_.Test Sinc At Zero()  Testnumericalstab|.Test Sinc At Zero() / Testnumericalstab]]
- [[_COMMUNITY_Estimate Correlation Time()  .Test Esti|Estimate Correlation Time() / .Test Esti]]
- [[_COMMUNITY_Parameter Names.Py  Verify Samples Dict|Parameter Names.Py / Verify Samples Dict]]
- [[_COMMUNITY_Testcrosscodingconsistency  Test Parame|Testcrosscodingconsistency / Test Parame]]
- [[_COMMUNITY_Testconfigvalidationlogging  .Test Conf|Testconfigvalidationlogging / .Test Conf]]
- [[_COMMUNITY_.Get Parameter Bounds()  .Get Active Pa|.Get Parameter Bounds() / .Get Active Pa]]
- [[_COMMUNITY_Testconfigboundsloading  Test Handling|Testconfigboundsloading / Test Handling ]]
- [[_COMMUNITY_Testparametercounts  .Test Total Count|Testparametercounts / .Test Total Count ]]
- [[_COMMUNITY_Testparametermanagerinit  .Test Init Wi|Testparametermanagerinit / .Test Init Wi]]
- [[_COMMUNITY_.Test Summary Values()  Testcmcresulted|.Test Summary Values() / Testcmcresulted]]
- [[_COMMUNITY_Should Use Pool()  .Test Pool Single Wo|Should Use Pool() / .Test Pool Single Wo]]
- [[_COMMUNITY_.  Init  ()  Testestimatephysicalworker|.  Init  () / Testestimatephysicalworker]]
- [[_COMMUNITY_Echo Worker()   Error Worker()| Echo Worker() /  Error Worker()]]
- [[_COMMUNITY_From Dict()  Is Enabled()|From Dict() / Is Enabled()]]
- [[_COMMUNITY_.Test Single Angle()  .Test Laminar Flo|.Test Single Angle() / .Test Laminar Flo]]
- [[_COMMUNITY_Testvalidatenonaninf  .Test Inf Detecte|Testvalidatenonaninf / .Test Inf Detecte]]
- [[_COMMUNITY_Testvalidateinitialparams  None Bounds|Testvalidateinitialparams / None Bounds ]]
- [[_COMMUNITY_Experimental Plots.Py  Plot Fit Compari|Experimental Plots.Py / Plot Fit Compari]]
- [[_COMMUNITY_Angle In Range()  Angle Filtering.Py|Angle In Range() / Angle Filtering.Py]]
- [[_COMMUNITY_.Test Estimate From Valid G2()  Testnls|.Test Estimate From Valid G2() / Testnls]]
- [[_COMMUNITY_.  Init  ()  Streamingexecutor|.  Init  () / Streamingexecutor]]
- [[_COMMUNITY_Testcmcargumentvalidation  .Test Valid|Testcmcargumentvalidation / .Test Valid ]]
- [[_COMMUNITY_Testcmcoptions  .Test Cmc Options Warne|Testcmcoptions / .Test Cmc Options Warne]]
- [[_COMMUNITY_.Test Method Mcmc Accepted()  .Test Met|.Test Method Mcmc Accepted() / .Test Met]]
- [[_COMMUNITY_Compute Uncertainties()  Testcomputeunc|Compute Uncertainties() / Testcomputeunc]]
- [[_COMMUNITY_.Test Scalar Layout Expanded()  Testext|.Test Scalar Layout Expanded() / Testext]]
- [[_COMMUNITY_Testextractnlsqmetadata   Extract Nlsq|Testextractnlsqmetadata /  Extract Nlsq ]]
- [[_COMMUNITY_Testpreparedata  Unique Phi Values Are|Testpreparedata / Unique Phi Values Are ]]
- [[_COMMUNITY_.Test Handles None Input()  Testtransfo|.Test Handles None Input() / Testtransfo]]
- [[_COMMUNITY_.To Original()  . Smooth Bound()|.To Original() / . Smooth Bound()]]
- [[_COMMUNITY_Testconfigwidthfactor  From Dict Uses 2|Testconfigwidthfactor / From Dict Uses 2]]
- [[_COMMUNITY_Testcvdispatchedgecases  .Test Cv With|Testcvdispatchedgecases / .Test Cv With ]]
- [[_COMMUNITY_Teststage6Effectivemodewithwarmstart  .|Teststage6Effectivemodewithwarmstart / .]]
- [[_COMMUNITY_Teststage7Nlsqpriorbuild  Build Nlsq In|Teststage7Nlsqpriorbuild / Build Nlsq In]]
- [[_COMMUNITY_Test Config.Py  Testreparameterizationc|Test Config.Py / Testreparameterizationc]]
- [[_COMMUNITY_Testparamawareshardsizing  .Test Scales|Testparamawareshardsizing / .Test Scales]]
- [[_COMMUNITY_Test Cli Commands.Py  Testconfiggenerat|Test Cli Commands.Py / Testconfiggenerat]]
- [[_COMMUNITY_Validation.Py  Validate Plot Arrays()|Validation.Py / Validate Plot Arrays()]]
- [[_COMMUNITY_Testpublicapistability  .Test Core Api|Testpublicapistability / .Test Core Api ]]
- [[_COMMUNITY_Static Plotting Config Section  Glossar|Static Plotting Config Section / Glossar]]
- [[_COMMUNITY_.Cleanup()  .  Init  ()|.Cleanup() / .  Init  ()]]
- [[_COMMUNITY_Out Of Core.Py   Effective Param Count|Out Of Core.Py /  Effective Param Count ]]
- [[_COMMUNITY_Main()  Run Benchmark()|Main() / Run Benchmark()]]
- [[_COMMUNITY_Testmoduleexports  Test Device Detectio|Testmoduleexports / Test Device Detectio]]
- [[_COMMUNITY_Init  ()  .Start Monitoring()|  Init  () / .Start Monitoring()]]
- [[_COMMUNITY_.  Init  ()  From Config()|.  Init  () / From Config()]]
- [[_COMMUNITY_.Get()  Cpuprofiler|.Get() / Cpuprofiler]]
- [[_COMMUNITY_Scalings()  Test Scaling.Py|Scalings() / Test Scaling.Py]]
- [[_COMMUNITY_Demo Forced Cmc()  Demo Forced Nuts()|Demo Forced Cmc() / Demo Forced Nuts()]]
- [[_COMMUNITY_Docs Index  Api Core Module|Docs Index / Api: Core Module]]
- [[_COMMUNITY_Test Suite Readme (V2.4.1, 47 Unit Files|Test Suite Readme (V2.4.1, 47 Unit Files]]
- [[_COMMUNITY_Nlsq Fit Quality Plot  Cmc Posterior Pl|Nlsq Fit Quality Plot / Cmc Posterior Pl]]
- [[_COMMUNITY_Numerical Correctness Tests  Testdiagon|Numerical Correctness Tests / Testdiagon]]
- [[_COMMUNITY_Time Array Should Start From 0.  Testti|Time Array Should Start From 0. / Testti]]
- [[_COMMUNITY_Testvalidationcomponentedgecases  .Test|Testvalidationcomponentedgecases / .Test]]
- [[_COMMUNITY_Testshearmodeledgecases  .Test Sinc Squ|Testshearmodeledgecases / .Test Sinc Squ]]
- [[_COMMUNITY_Testgradientwithrealparameters  .Test N|Testgradientwithrealparameters / .Test N]]
- [[_COMMUNITY_.Get Cmc Config()  . Merge Cmc Config()|.Get Cmc Config() / . Merge Cmc Config()]]
- [[_COMMUNITY_Testintegrationscenarios  .Test Explora|Testintegrationscenarios / .Test Explora]]
- [[_COMMUNITY_Testmissingrequiredfields  .Test Parame|Testmissingrequiredfields / .Test Parame]]
- [[_COMMUNITY_Testnlsqconfigvalidation  Tests For T09|Testnlsqconfigvalidation / Tests For T09]]
- [[_COMMUNITY_Testinitialparametersloading  .Test Val|Testinitialparametersloading / .Test Val]]
- [[_COMMUNITY_Testedgecases  .Test Zero Values()|Testedgecases / .Test Zero Values()]]
- [[_COMMUNITY_Testconfignormalization  .Test Normaliz|Testconfignormalization / .Test Normaliz]]
- [[_COMMUNITY_.Test Static Mode Parameters()  .Test L|.Test Static Mode Parameters() / .Test L]]
- [[_COMMUNITY_Testactiveparameters  Test Active Param|Testactiveparameters / Test Active Param]]
- [[_COMMUNITY_. Build Z Space Init()  Testreparamwarm|. Build Z Space Init() / Testreparamwarm]]
- [[_COMMUNITY_Jacobian.Py  Compute Jacobian Stats()|Jacobian.Py / Compute Jacobian Stats()]]
- [[_COMMUNITY_.  Exit  ()  .Shutdown()|.  Exit  () / .Shutdown()]]
- [[_COMMUNITY_Stratified Ls.Py  Create Stratified Chu|Stratified Ls.Py / Create Stratified Chu]]
- [[_COMMUNITY_Main()  Diagnostics.Py|Main() / Diagnostics.Py]]
- [[_COMMUNITY_.Test Empty Xdata Fails()  .Test Empty|.Test Empty Xdata Fails() / .Test Empty ]]
- [[_COMMUNITY_Testmoduleexports  Test Nlsq Validation|Testmoduleexports / Test Nlsq Validation]]
- [[_COMMUNITY_.Test Security Edge Cases()  .Test Vali|.Test Security Edge Cases() / .Test Vali]]
- [[_COMMUNITY_Testdevicebenchmarking  Benchmark Devic|Testdevicebenchmarking / Benchmark Devic]]
- [[_COMMUNITY_.  Init  ()  Memorystats|.  Init  () / Memorystats]]
- [[_COMMUNITY_.  Init  ()  Parameterspace|.  Init  () / Parameterspace]]
- [[_COMMUNITY_Testrandomgeneration  Generate Random S|Testrandomgeneration / Generate Random S]]
- [[_COMMUNITY_Testhandlenlsqresult  .Test Invalid Tup|Testhandlenlsqresult / .Test Invalid Tup]]
- [[_COMMUNITY_Largedatasetexecutor  Testlargedatasete|Largedatasetexecutor / Testlargedatasete]]
- [[_COMMUNITY_.Test Shear Rate Alias()  .Test Trapezo|.Test Shear Rate Alias() / .Test Trapezo]]
- [[_COMMUNITY_Physics Utils.Py  Testcalculateshearrat|Physics Utils.Py / Testcalculateshearrat]]
- [[_COMMUNITY_Testdeprecatedmethodrejection  .Test Me|Testdeprecatedmethodrejection / .Test Me]]
- [[_COMMUNITY_Testprepareparameterdata   Prepare Para|Testprepareparameterdata /  Prepare Para]]
- [[_COMMUNITY_Testgetphysicalparamcount  Get Physical|Testgetphysicalparamcount / Get Physical]]
- [[_COMMUNITY_Testbuildresult  Tests For  Build Resul|Testbuildresult / Tests For  Build Resul]]
- [[_COMMUNITY_.  Repr  ()  .Get Statistics()|.  Repr  () / .Get Statistics()]]
- [[_COMMUNITY_Test Residual Function.Py  Testresidual|Test Residual Function.Py / Testresidual]]
- [[_COMMUNITY_Testnlsqwrappererrorhandling  .Test Err|Testnlsqwrappererrorhandling / .Test Err]]
- [[_COMMUNITY_Mock Config()  Mock Xpcs Data()|Mock Config() / Mock Xpcs Data()]]
- [[_COMMUNITY_.  Init  ()  .Get Prior()|.  Init  () / .Get Prior()]]
- [[_COMMUNITY_Testpriortemperingscale  .Test Prior Sc|Testpriortemperingscale / .Test Prior Sc]]
- [[_COMMUNITY_Testpriortemperingconfig  .Test Config|Testpriortemperingconfig / .Test Config ]]
- [[_COMMUNITY_Testyamlescapestring   Yaml Escape Stri|Testyamlescapestring /  Yaml Escape Stri]]
- [[_COMMUNITY_Syntheticxpcsdata  Synthetic Data.Py|Syntheticxpcsdata / Synthetic Data.Py]]
- [[_COMMUNITY_Testmcmcmoduleavailability  .Test Cmc M|Testmcmcmoduleavailability / .Test Cmc M]]
- [[_COMMUNITY_Testversioncompatibility  .Test Version|Testversioncompatibility / .Test Version]]
- [[_COMMUNITY_Testmcmccompatibility  Testsaveresultss|Testmcmccompatibility / Testsaveresultss]]
- [[_COMMUNITY_Main()  Compute C2 Cmc()|Main() / Compute C2 Cmc()]]
- [[_COMMUNITY_Main()  Run Nlsq Fit()|Main() / Run Nlsq Fit()]]
- [[_COMMUNITY_Correlation Functions Theory  Theoretic|Correlation Functions Theory / Theoretic]]
- [[_COMMUNITY_Configmanager Class  Batch Processing G|Configmanager Class / Batch Processing G]]
- [[_COMMUNITY_Scripts And Demos Readme  Scripts Benc|Scripts And Demos Readme / Scripts: Benc]]
- [[_COMMUNITY_Init  .Py    Getattr  ()|  Init  .Py /   Getattr  ()]]
- [[_COMMUNITY_Config.Py  .Is Valid()|Config.Py / .Is Valid()]]
- [[_COMMUNITY_.  Init  ()  .Get Prior()|.  Init  () / .Get Prior()]]
- [[_COMMUNITY_Adapter()  Testinheritance|Adapter() / Testinheritance]]
- [[_COMMUNITY_Mock Parameter Space()  Testscalingutil|Mock Parameter Space() / Testscalingutil]]
- [[_COMMUNITY_Main()  Run Benchmark()|Main() / Run Benchmark()]]
- [[_COMMUNITY_Cmc Prior Tempering  Gradient-Safe Floo|Cmc Prior Tempering / Gradient-Safe Floo]]
- [[_COMMUNITY_VizNlsq Plots.Py  VizMcmc Dashboard.P|Viz/Nlsq Plots.Py / Viz/Mcmc Dashboard.P]]
- [[_COMMUNITY_Ess And Bfmi Mcmc Diagnostics  Nuts (No|Ess And Bfmi Mcmc Diagnostics / Nuts (No]]
- [[_COMMUNITY_Nlsq Warm-Start For Cmc  Adr-001 Jax C|Nlsq Warm-Start For Cmc / Adr-001: Jax C]]
- [[_COMMUNITY_Glossary Term Nuts (No-U-Turn Sampler)|Glossary Term: Nuts (No-U-Turn Sampler) ]]
- [[_COMMUNITY_Troubleshooting Shell Completion Issues|Troubleshooting: Shell Completion Issues]]
- [[_COMMUNITY_Main()  Get Xla Mode Path()|Main() / Get Xla Mode Path()]]
- [[_COMMUNITY_Install Xla Activation()  Get Xla Confi|Install Xla Activation() / Get Xla Confi]]
- [[_COMMUNITY_Testunifiedmodulebackends  .Test Numpy|Testunifiedmodulebackends / .Test Numpy ]]
- [[_COMMUNITY_Testjaxbackendedgecases  .Test Jit Comp|Testjaxbackendedgecases / .Test Jit Comp]]
- [[_COMMUNITY_Testparameterinfoedgecases  .Test Get P|Testparameterinfoedgecases / .Test Get P]]
- [[_COMMUNITY_Testgradientsanitycheck  .Test Gradient|Testgradientsanitycheck / .Test Gradient]]
- [[_COMMUNITY_Testregressionprevention  .Test No Phi|Testregressionprevention / .Test No Phi ]]
- [[_COMMUNITY_Testfullmcmcworkflow  .Test Config Driv|Testfullmcmcworkflow / .Test Config Driv]]
- [[_COMMUNITY_Testconfigmanageractiveparameters  .Tes|Testconfigmanageractiveparameters / .Tes]]
- [[_COMMUNITY_.Test From Defaults Static()  Testparam|.Test From Defaults Static() / Testparam]]
- [[_COMMUNITY_Testconfigmanagerparameterbounds  Test|Testconfigmanagerparameterbounds / Test ]]
- [[_COMMUNITY_Testinfolevelviolations  .Test Very Low|Testinfolevelviolations / .Test Very Low]]
- [[_COMMUNITY_Testseverityfiltering  .Test Info Level|Testseverityfiltering / .Test Info Level]]
- [[_COMMUNITY_Testfixedparameters  .Test Get Fixed Pa|Testfixedparameters / .Test Get Fixed Pa]]
- [[_COMMUNITY_Testparameteractivestatus  .Test Parame|Testparameteractivestatus / .Test Parame]]
- [[_COMMUNITY_Testoptimizableparameters  .Test Optimi|Testoptimizableparameters / .Test Optimi]]
- [[_COMMUNITY_Testvalidationmessages  .Test Failure M|Testvalidationmessages / .Test Failure M]]
- [[_COMMUNITY_Testedgecases  .Test Empty Config()|Testedgecases / .Test Empty Config()]]
- [[_COMMUNITY_Testparametervalidation  .Test Validate|Testparametervalidation / .Test Validate]]
- [[_COMMUNITY_Main()  Baselinemetrics|Main() / Baselinemetrics]]
- [[_COMMUNITY_Testparallelthreshold  .Test Below Thre|Testparallelthreshold / .Test Below Thre]]
- [[_COMMUNITY_Main()  Main.Py|Main() / Main.Py]]
- [[_COMMUNITY_. Check Pressure Levels()  . Trigger Wa|. Check Pressure Levels() / . Trigger Wa]]
- [[_COMMUNITY_Optimizationexecutor  .Test Executor Is|Optimizationexecutor / .Test Executor Is]]
- [[_COMMUNITY_.Test Repr()  .Test Config Summary()|.Test Repr() / .Test Config Summary()]]
- [[_COMMUNITY_.Compute C2()  .Plot Simulated Data()|.Compute C2() / .Plot Simulated Data()]]
- [[_COMMUNITY_Testcmaesdiagonalfiltering  .Test Diago|Testcmaesdiagonalfiltering / .Test Diago]]
- [[_COMMUNITY_Vmap()  Testdispatchermemory|Vmap() / Testdispatchermemory]]
- [[_COMMUNITY_Testdataloadingintegration  .Test Compl|Testdataloadingintegration / .Test Compl]]
- [[_COMMUNITY_Testhelptextdocumentation  .Test Cmc Gr|Testhelptextdocumentation / .Test Cmc Gr]]
- [[_COMMUNITY_.Test Mcmc Chains Validation()  .Test M|.Test Mcmc Chains Validation() / .Test M]]
- [[_COMMUNITY_Testhelptextvalidation  .Test Cmc Group|Testhelptextvalidation / .Test Cmc Group]]
- [[_COMMUNITY_Testshellaliasdefinitions  .Test Shell|Testshellaliasdefinitions / .Test Shell ]]
- [[_COMMUNITY_Testcmcspecificoptions  .Test All Cmc O|Testcmcspecificoptions / .Test All Cmc O]]
- [[_COMMUNITY_Testqualitymetrics  Test Result Builder|Testqualitymetrics / Test Result Builder]]
- [[_COMMUNITY_Testnlsqadapterbase  .Test Is Abstract|Testnlsqadapterbase / .Test Is Abstract ]]
- [[_COMMUNITY_Testsetupbounds  .Test Setup Bounds Fro|Testsetupbounds / .Test Setup Bounds Fro]]
- [[_COMMUNITY_Test Adapter Base.Py  Testadapterinheri|Test Adapter Base.Py / Testadapterinheri]]
- [[_COMMUNITY_Testsharedmethodimplementation  Test Th|Testsharedmethodimplementation / Test Th]]
- [[_COMMUNITY_Testcomputecovariance  Covariance Is Co|Testcomputecovariance / Covariance Is Co]]
- [[_COMMUNITY_Testboundsformatconversion  .Test None|Testboundsformatconversion / .Test None ]]
- [[_COMMUNITY_Testdataflattening  .Test Empty Data Ha|Testdataflattening / .Test Empty Data Ha]]
- [[_COMMUNITY_Create Disabled Filtering Config()  .Te|Create Disabled Filtering Config() / .Te]]
- [[_COMMUNITY_Testnlsqconfigisvalid  Test Default Con|Testnlsqconfigisvalid / Test Default Con]]
- [[_COMMUNITY_Test Nlsq Config.Py  Testnlsqconfigvali|Test Nlsq Config.Py / Testnlsqconfigvali]]
- [[_COMMUNITY_Scaling Utils.Py  Compute Averaged Scal|Scaling Utils.Py / Compute Averaged Scal]]
- [[_COMMUNITY_Testcmcresultmethods  .Test Get Posteri|Testcmcresultmethods / .Test Get Posteri]]
- [[_COMMUNITY_Teststage2Robustconsensus  .Test Class|Teststage2Robustconsensus / .Test Class ]]
- [[_COMMUNITY_Teststage1Numchainsdefault  .Test Defau|Teststage1Numchainsdefault / .Test Defau]]
- [[_COMMUNITY_Testboundsawarecv  Test Heterogeneity F|Testboundsawarecv / Test Heterogeneity F]]
- [[_COMMUNITY_Testcliquietflag  .Test Quiet Config Va|Testcliquietflag / .Test Quiet Config Va]]
- [[_COMMUNITY_Testmultiprocessinglogging  .Test With|Testmultiprocessinglogging / .Test With ]]
- [[_COMMUNITY_Testfunctionsignatures  .Test Data Load|Testfunctionsignatures / .Test Data Load]]
- [[_COMMUNITY_Main()  Load Shard()|Main() / Load Shard()]]
- [[_COMMUNITY_Model()  Test Homodyne Model.Py|Model() / Test Homodyne Model.Py]]
- [[_COMMUNITY_.Build()  Qualitymetrics|.Build() / Qualitymetrics]]
- [[_COMMUNITY_Release V2.22.9  System Overview|Release V2.22.9 / System Overview]]
- [[_COMMUNITY_Api Cli  Cli Data Pipeline|Api: Cli / Cli Data Pipeline]]
- [[_COMMUNITY_Testing Guide  Contributing Guide|Testing Guide / Contributing Guide]]
- [[_COMMUNITY_Testnlsqdiagonalmasking  .Test Diagonal|Testnlsqdiagonalmasking / .Test Diagonal]]
- [[_COMMUNITY_Init  .Py  Get Optimization Info()|  Init  .Py / Get Optimization Info()]]
- [[_COMMUNITY_Teststage4Constantaveragedscaling  .Tes|Teststage4Constantaveragedscaling / .Tes]]
- [[_COMMUNITY_Testbuildinitvaluesdict  .Test Constant|Testbuildinitvaluesdict / .Test Constant]]
- [[_COMMUNITY_N Workers()  Result Queue()|N Workers() / Result Queue()]]
- [[_COMMUNITY_.  Init  ()  . Determine Mode()|.  Init  () / . Determine Mode()]]
- [[_COMMUNITY_.Log Summary()  .Compute Regularization|.Log Summary() / .Compute Regularization]]
- [[_COMMUNITY_Order()  From Dict()|Order() / From Dict()]]
- [[_COMMUNITY_Init  .Py  Get Completion Script()|  Init  .Py / Get Completion Script()]]
- [[_COMMUNITY_Testbackwardcompatibility  .Test Existi|Testbackwardcompatibility / .Test Existi]]
- [[_COMMUNITY_Data Pipeline.Py   Pool Mcmc Data()|Data Pipeline.Py /  Pool Mcmc Data()]]
- [[_COMMUNITY_.Get Memory Stats()  .Get Pressure Tren|.Get Memory Stats() / .Get Pressure Tren]]
- [[_COMMUNITY_Allocationerror  . Allocate Buffer()|Allocationerror / . Allocate Buffer()]]
- [[_COMMUNITY_Test Executors.Py  Testexecutorerrorhan|Test Executors.Py / Testexecutorerrorhan]]
- [[_COMMUNITY_.Test Very Small Dt()  .Test Single Tim|.Test Very Small Dt() / .Test Single Tim]]
- [[_COMMUNITY_Testjaxbackendfallback  .Test Numpy Com|Testjaxbackendfallback / .Test Numpy Com]]
- [[_COMMUNITY_Testparameterdependency  .Test G2 Gradi|Testparameterdependency / .Test G2 Gradi]]
- [[_COMMUNITY_Testconstants  .Test Pi Value()|Testconstants / .Test Pi Value()]]
- [[_COMMUNITY_Testconfigfilevalidation  .Test Missing|Testconfigfilevalidation / .Test Missing]]
- [[_COMMUNITY_Testconflictingarguments  .Test Verbose|Testconflictingarguments / .Test Verbose]]
- [[_COMMUNITY_Testdefaultconfigbehavior  Test Default|Testdefaultconfigbehavior / Test Default]]
- [[_COMMUNITY_Testclihelpoutput  .Test Homodyne Help|Testclihelpoutput / .Test Homodyne Help ]]
- [[_COMMUNITY_Testmethodvalidation  .Test Validate Ar|Testmethodvalidation / .Test Validate Ar]]
- [[_COMMUNITY_Create Overlapping Ranges Config()  .Te|Create Overlapping Ranges Config() / .Te]]
- [[_COMMUNITY_Scaling.Py  Log Scaling Factors()|Scaling.Py / Log Scaling Factors()]]
- [[_COMMUNITY_Testmodelnumshardsparameter  .Test Aver|Testmodelnumshardsparameter / .Test Aver]]
- [[_COMMUNITY_.  Init  ()   Fakecmcresult|.  Init  () /  Fakecmcresult]]
- [[_COMMUNITY_Test Plots.Py  Testnlsqplotscontrastwar|Test Plots.Py / Testnlsqplotscontrastwar]]
- [[_COMMUNITY_Testcliverboseflag  .Test Verbose Enabl|Testcliverboseflag / .Test Verbose Enabl]]
- [[_COMMUNITY_Testreturntypes  Test Compatibility.Py|Testreturntypes / Test Compatibility.Py]]
- [[_COMMUNITY_Testdeprecationwarnings  Test Deprecati|Testdeprecationwarnings / Test Deprecati]]
- [[_COMMUNITY_Testrealdatastratification  Test Real D|Testrealdatastratification / Test Real D]]
- [[_COMMUNITY_Main()  Compute C2 Cmc()|Main() / Compute C2 Cmc()]]
- [[_COMMUNITY_Manager.Py  Get Logger()|Manager.Py / Get Logger()]]
- [[_COMMUNITY_.To Dict()  Memoryprofile|.To Dict() / Memoryprofile]]
- [[_COMMUNITY_Sample Result()  Test Results.Py|Sample Result() / Test Results.Py]]
- [[_COMMUNITY_Meshgrid Lru Cache  Jax Computational K|Meshgrid Lru Cache / Jax Computational K]]
- [[_COMMUNITY_L()  N()|L() / N()]]
- [[_COMMUNITY_Analysis Modes (Static, Laminar Flow)|Analysis Modes (Static, Laminar Flow) / ]]
- [[_COMMUNITY_Yaml Template Homodyne Laminar Flow.Yam|Yaml Template: Homodyne Laminar Flow.Yam]]
- [[_COMMUNITY_.  Init  ()  Filtercriteria|.  Init  () / Filtercriteria]]
- [[_COMMUNITY_.  Init  ()  . Parse Config()|.  Init  () / . Parse Config()]]
- [[_COMMUNITY_.To Dict()  .Save Provenance()|.To Dict() / .Save Provenance()]]
- [[_COMMUNITY_.Log Summary()  .Get Diagnostics()|.Log Summary() / .Get Diagnostics()]]
- [[_COMMUNITY_.Per Angle To Fourier()  .Get Initial C|.Per Angle To Fourier() / .Get Initial C]]
- [[_COMMUNITY_Mcmc Comparison.Py  Plot Posterior Comp|Mcmc Comparison.Py / Plot Posterior Comp]]
- [[_COMMUNITY_Mcmc Dashboard.Py  Plot Cmc Summary Das|Mcmc Dashboard.Py / Plot Cmc Summary Das]]
- [[_COMMUNITY_Testcmcwarningswithnlsq  .Test Cmc Opti|Testcmcwarningswithnlsq / .Test Cmc Opti]]
- [[_COMMUNITY_Args Parser.Py  Create Parser()|Args Parser.Py / Create Parser()]]
- [[_COMMUNITY_.To Dict()  Timingbreakdown|.To Dict() / Timingbreakdown]]
- [[_COMMUNITY_.To Normalized()  . Smooth Bound Invers|.To Normalized() / . Smooth Bound Invers]]
- [[_COMMUNITY_Conftest.Py  Pytest Collection Modifyit|Conftest.Py / Pytest Collection Modifyit]]
- [[_COMMUNITY_Phaserecord  .Start Phase()| Phaserecord / .Start Phase()]]
- [[_COMMUNITY_Conftest.Py  Synthetic Xpcs Data()|Conftest.Py / Synthetic Xpcs Data()]]
- [[_COMMUNITY_Testerrorhandling  Test Error Handling|Testerrorhandling / Test Error Handling ]]
- [[_COMMUNITY_.Test Basic Usage Example()  Testdocume|.Test Basic Usage Example() / Testdocume]]
- [[_COMMUNITY_Sub-Diffusion (0  Alpha  1)  Classica|Sub-Diffusion (0 < Alpha < 1) / Classica]]
- [[_COMMUNITY_Init  .Py    Init  .Py|  Init  .Py /   Init  .Py]]
- [[_COMMUNITY_Init  .Py    Init  .Py|  Init  .Py /   Init  .Py]]
- [[_COMMUNITY_Init  .Py   Note Datasetsizestrateg|  Init  .Py / # Note: Datasetsizestrateg]]
- [[_COMMUNITY_Init  .Py    Init  .Py|  Init  .Py /   Init  .Py]]
- [[_COMMUNITY_Init  .Py   Missing Datashader()|  Init  .Py /  Missing Datashader()]]
- [[_COMMUNITY_Config Summary()  Homodyne Model.Py|Config Summary() / Homodyne Model.Py]]
- [[_COMMUNITY_Main()  Streaming 100M Points.Py|Main() / Streaming 100M Points.Py]]
- [[_COMMUNITY_Main()  Laminar Flow Nlsq.Py|Main() / Laminar Flow Nlsq.Py]]
- [[_COMMUNITY_Main()  Static Isotropic Nlsq.Py|Main() / Static Isotropic Nlsq.Py]]
- [[_COMMUNITY_Main()  Angle Filtering.Py|Main() / Angle Filtering.Py]]
- [[_COMMUNITY_Main()  Mcmc Uncertainty.Py|Main() / Mcmc Uncertainty.Py]]
- [[_COMMUNITY_Main()  Cmc Large Dataset.Py|Main() / Cmc Large Dataset.Py]]
- [[_COMMUNITY_Consensus Monte Carlo  Precompute Shard|Consensus Monte Carlo / Precompute Shard]]
- [[_COMMUNITY_Fourierreparameterizer Class  Fourier B|Fourierreparameterizer Class / Fourier B]]
- [[_COMMUNITY_Init  .Py  Core Computation Engine Fo|  Init  .Py / Core Computation Engine Fo]]
- [[_COMMUNITY_.Test None Result Not Queued()  Test Th|.Test None Result Not Queued() / Test Th]]
- [[_COMMUNITY_Init  .Py  Cmc Execution Backends.  T|  Init  .Py / Cmc Execution Backends.  T]]
- [[_COMMUNITY_.Compute Regularization Jax()  Compute|.Compute Regularization Jax() / Compute ]]
- [[_COMMUNITY_.Get Basis Matrix()  Get The Fourier Ba|.Get Basis Matrix() / Get The Fourier Ba]]
- [[_COMMUNITY_.Test Constraint Violation Check()  T05|.Test Constraint Violation Check() / T05]]
- [[_COMMUNITY_.Test Diagnostics()  T051E Test Diagno|.Test Diagnostics() / T051E: Test Diagno]]
- [[_COMMUNITY_.Get Coefficient Labels()  Get Paramete|.Get Coefficient Labels() / Get Paramete]]
- [[_COMMUNITY_.Get Jacobian Transform()  Get Jacobian|.Get Jacobian Transform() / Get Jacobian]]
- [[_COMMUNITY_.Test From Dict()  T057B Test Config C|.Test From Dict() / T057B: Test Config C]]
- [[_COMMUNITY_.Get Diagnostics()  Get Regularization|.Get Diagnostics() / Get Regularization ]]
- [[_COMMUNITY_.  Init  ()  Initialize Adaptive Regula|.  Init  () / Initialize Adaptive Regula]]
- [[_COMMUNITY_.Test Fit Convergence()  T051D Test Hi|.Test Fit Convergence() / T051D: Test Hi]]
- [[_COMMUNITY_.Reset()  Reset Monitor State For New O|.Reset() / Reset Monitor State For New O]]
- [[_COMMUNITY_.Test From Dict Safe Conversion()  T053|.Test From Dict Safe Conversion() / T053]]
- [[_COMMUNITY_.Test Regularizer Lambda Autotuned()  T|.Test Regularizer Lambda Autotuned() / T]]
- [[_COMMUNITY_.Test Gradient Collapse Detection In Fou|.Test Gradient Collapse Detection In Fou]]
- [[_COMMUNITY_.Test Regularization Gradient()  T052E|.Test Regularization Gradient() / T052E:]]
- [[_COMMUNITY_.Test From Dict Safe Conversion()  T052|.Test From Dict Safe Conversion() / T052]]
- [[_COMMUNITY_.Test From Dict()  T050B Test Config C|.Test From Dict() / T050B: Test Config C]]
- [[_COMMUNITY_.Test From Dict Safe Conversion()  T051|.Test From Dict Safe Conversion() / T051]]
- [[_COMMUNITY_.Test Hierarchical Uses Fourier Indices(|.Test Hierarchical Uses Fourier Indices(]]
- [[_COMMUNITY_.Test Parameter Indices()  T051C Test|.Test Parameter Indices() / T051C: Test ]]
- [[_COMMUNITY_.  Init  ()  Initialize Hierarchical Op|.  Init  () / Initialize Hierarchical Op]]
- [[_COMMUNITY_.Get Bounds()  Get Bounds For Fourier C|.Get Bounds() / Get Bounds For Fourier C]]
- [[_COMMUNITY_.Test Full Pipeline Synthetic Data()  T|.Test Full Pipeline Synthetic Data() / T]]
- [[_COMMUNITY_.Compute Regularization Gradient()  Com|.Compute Regularization Gradient() / Com]]
- [[_COMMUNITY_.Get Diagnostics()  Get Optimizer Diagn|.Get Diagnostics() / Get Optimizer Diagn]]
- [[_COMMUNITY_.Test Fourier Reduces Params From 46 To|.Test Fourier Reduces Params From 46 To ]]
- [[_COMMUNITY_.Test Cv Based Regularization()  T052D|.Test Cv Based Regularization() / T052D:]]
- [[_COMMUNITY_.Get Diagnostics()  Get Fourier Reparam|.Get Diagnostics() / Get Fourier Reparam]]
- [[_COMMUNITY_.Test Cv Constraint Violation Detection(|.Test Cv Constraint Violation Detection(]]
- [[_COMMUNITY_.Test Diagnostics Output()  T056G All|.Test Diagnostics Output() / T056G: All ]]
- [[_COMMUNITY_.Compute Reset Params()  Compute Parame|.Compute Reset Params() / Compute Parame]]
- [[_COMMUNITY_.Test Auto Tuned Lambda()  T052C Test|.Test Auto Tuned Lambda() / T052C: Test ]]
- [[_COMMUNITY_.  Init  ()  Initialize Gradient Collap|.  Init  () / Initialize Gradient Collap]]
- [[_COMMUNITY_.Get Response()  Get Response Action Af|.Get Response() / Get Response Action Af]]
- [[_COMMUNITY_Init  .Py  Validation Utilities For N|  Init  .Py / Validation Utilities For N]]
- [[_COMMUNITY_Init  .Py  IO Operations For Homodyn|  Init  .Py / I/O Operations For Homodyn]]
- [[_COMMUNITY_Init  .Py  Runtime Utilities For Homo|  Init  .Py / Runtime Utilities For Homo]]
- [[_COMMUNITY_Init  .Py  Shell Activation Scripts F|  Init  .Py / Shell Activation Scripts F]]
- [[_COMMUNITY_Init  .Py  Command Line Interface For|  Init  .Py / Command Line Interface For]]
- [[_COMMUNITY_Mcmc Plots.Py  Mcmc Diagnostic Visualiz|Mcmc Plots.Py / Mcmc Diagnostic Visualiz]]
- [[_COMMUNITY_Init  .Py  Homodyne Test Suite ======|  Init  .Py / Homodyne Test Suite ======]]
- [[_COMMUNITY_.Test Chunked Strategy Progress Info()|.Test Chunked Strategy Progress Info() /]]
- [[_COMMUNITY_.Test Scalar Popt Converted To Array()|.Test Scalar Popt Converted To Array() /]]
- [[_COMMUNITY_.Test Object With All Common Attributes(|.Test Object With All Common Attributes(]]
- [[_COMMUNITY_.Test List Converted To Array()  Test T|.Test List Converted To Array() / Test T]]
- [[_COMMUNITY_.Test Tuple Three Elements Empty Info()|.Test Tuple Three Elements Empty Info() ]]
- [[_COMMUNITY_.Test Object With X Attribute()  Test O|.Test Object With X Attribute() / Test O]]
- [[_COMMUNITY_.Test Dict Missing Pcov Creates Identity|.Test Dict Missing Pcov Creates Identity]]
- [[_COMMUNITY_.Test Popt Pcov Dimension Consistency()|.Test Popt Pcov Dimension Consistency() ]]
- [[_COMMUNITY_.Test Nlsq V015 Streaming Optimizer()|.Test Nlsq V015 Streaming Optimizer() / ]]
- [[_COMMUNITY_Test Large Strategy Can Return Object.|Test Large Strategy Can Return Object. /]]
- [[_COMMUNITY_Test Dict With Partial Streaming Diagnos|Test Dict With Partial Streaming Diagnos]]
- [[_COMMUNITY_.Test None Result Raises Error()  Test|.Test None Result Raises Error() / Test ]]
- [[_COMMUNITY_.Test Nlsq V015 Curve Fit Large()  Mock|.Test Nlsq V015 Curve Fit Large() / Mock]]
- [[_COMMUNITY_.Test Dict Missing Both X And Popt Raise|.Test Dict Missing Both X And Popt Raise]]
- [[_COMMUNITY_.Test Tuple Three Elements With Info()|.Test Tuple Three Elements With Info() /]]
- [[_COMMUNITY_.Test Unrecognized Type Raises Error()|.Test Unrecognized Type Raises Error() /]]
- [[_COMMUNITY_.Test Identity Pcov When Missing Has Cor|.Test Identity Pcov When Missing Has Cor]]
- [[_COMMUNITY_.Test Object Missing Pcov Creates Identi|.Test Object Missing Pcov Creates Identi]]
- [[_COMMUNITY_.Test Nlsq V015 Curve Fit With Full Outp|.Test Nlsq V015 Curve Fit With Full Outp]]
- [[_COMMUNITY_.Test Dict With Popt Fallback()  Test D|.Test Dict With Popt Fallback() / Test D]]
- [[_COMMUNITY_Test Object Without 'X' Or 'Popt' Raises|Test Object Without 'X' Or 'Popt' Raises]]
- [[_COMMUNITY_.Test Nlsq V015 Curve Fit Standard()  M|.Test Nlsq V015 Curve Fit Standard() / M]]
- [[_COMMUNITY_.Test Large Parameter Count()  Test Han|.Test Large Parameter Count() / Test Han]]
- [[_COMMUNITY_.Test Dict With X And Pcov()  Test Dict|.Test Dict With X And Pcov() / Test Dict]]
- [[_COMMUNITY_.Test Streaming Strategy With Full Diagn|.Test Streaming Strategy With Full Diagn]]
- [[_COMMUNITY_.Test Empty Tuple Raises Error()  Test|.Test Empty Tuple Raises Error() / Test ]]
- [[_COMMUNITY_.Test Tuple Two Elements Standard()  Te|.Test Tuple Two Elements Standard() / Te]]
- [[_COMMUNITY_.Test Preserves Array Dtype()  Test Tha|.Test Preserves Array Dtype() / Test Tha]]
- [[_COMMUNITY_.Test Object With Popt Attribute()  Tes|.Test Object With Popt Attribute() / Tes]]
- [[_COMMUNITY_Init  .Py  Unit Tests For Homodyne Co|  Init  .Py / Unit Tests For Homodyne Co]]
- [[_COMMUNITY_.Test R Hat Values()  Test R Hat Contai|.Test R Hat Values() / Test R Hat Contai]]
- [[_COMMUNITY_.Test Heartbeat Timeout Validation()  T|.Test Heartbeat Timeout Validation() / T]]
- [[_COMMUNITY_.Test From Dict None()  Test Creating C|.Test From Dict None() / Test Creating C]]
- [[_COMMUNITY_.Test Chain Method Validation Valid()|.Test Chain Method Validation Valid() / ]]
- [[_COMMUNITY_.Test Chain Method From Dict Default()|.Test Chain Method From Dict Default() /]]
- [[_COMMUNITY_.Test From Dict Nested Sharding()  Test|.Test From Dict Nested Sharding() / Test]]
- [[_COMMUNITY_.Test Validate Invalid Samples()  Test|.Test Validate Invalid Samples() / Test ]]
- [[_COMMUNITY_.Test Chain Method To Dict()  Test Chai|.Test Chain Method To Dict() / Test Chai]]
- [[_COMMUNITY_.Test Validate Invalid Accept Prob()  T|.Test Validate Invalid Accept Prob() / T]]
- [[_COMMUNITY_.Test To Dict Includes New Fields()  Te|.Test To Dict Includes New Fields() / Te]]
- [[_COMMUNITY_.Test Heartbeat Timeout Default()  Test|.Test Heartbeat Timeout Default() / Test]]
- [[_COMMUNITY_.Test Should Enable Cmc Auto Large Data(|.Test Should Enable Cmc Auto Large Data(]]
- [[_COMMUNITY_.Test Default Chain Method()  Test That|.Test Default Chain Method() / Test That]]
- [[_COMMUNITY_.Test Should Enable Cmc Auto Small Data(|.Test Should Enable Cmc Auto Small Data(]]
- [[_COMMUNITY_.Test Validate No Errors()  Test Valida|.Test Validate No Errors() / Test Valida]]
- [[_COMMUNITY_.Test Chain Method Validation Invalid()|.Test Chain Method Validation Invalid() ]]
- [[_COMMUNITY_.Test From Dict Basic()  Test Creating|.Test From Dict Basic() / Test Creating ]]
- [[_COMMUNITY_.Test Min Success Rate Warning Default()|.Test Min Success Rate Warning Default()]]
- [[_COMMUNITY_.Test Validate Invalid Chains()  Test V|.Test Validate Invalid Chains() / Test V]]
- [[_COMMUNITY_.Test Should Enable Cmc Explicit True()|.Test Should Enable Cmc Explicit True() ]]
- [[_COMMUNITY_.Test Integer Array Is Clean()  Test Th|.Test Integer Array Is Clean() / Test Th]]
- [[_COMMUNITY_.Test Single Element Array()  Test Vali|.Test Single Element Array() / Test Vali]]
- [[_COMMUNITY_.Test Array With Nan Returns False()  T|.Test Array With Nan Returns False() / T]]
- [[_COMMUNITY_.Test Negative Values Are Valid()  Test|.Test Negative Values Are Valid() / Test]]
- [[_COMMUNITY_.Test Very Large Values Are Valid()  Te|.Test Very Large Values Are Valid() / Te]]
- [[_COMMUNITY_.Test Names Longer Than Arrays()  Test|.Test Names Longer Than Arrays() / Test ]]
- [[_COMMUNITY_.Test Single Nan Element()  Test Valida|.Test Single Nan Element() / Test Valida]]
- [[_COMMUNITY_.Test 2D Array Clean()  Test Validation|.Test 2D Array Clean() / Test Validation]]
- [[_COMMUNITY_.Test With Named Arrays()  Test Validat|.Test With Named Arrays() / Test Validat]]
- [[_COMMUNITY_.Test Empty Array Is Clean()  Test That|.Test Empty Array Is Clean() / Test That]]
- [[_COMMUNITY_.Test Mixed Nan And Inf()  Test Array W|.Test Mixed Nan And Inf() / Test Array W]]
- [[_COMMUNITY_.Test Zero Values Are Valid()  Test Tha|.Test Zero Values Are Valid() / Test Tha]]
- [[_COMMUNITY_.Test All Nan Array()  Test Array With|.Test All Nan Array() / Test Array With ]]
- [[_COMMUNITY_.Test Clean Array Returns True()  Test|.Test Clean Array Returns True() / Test ]]
- [[_COMMUNITY_Init  .Py  Integration Tests For Homo|  Init  .Py / Integration Tests For Homo]]
- [[_COMMUNITY_Init  .Py  Test Data Factories For Ho|  Init  .Py / Test Data Factories For Ho]]
- [[_COMMUNITY_Init  .Py  Mcmc Statistical Tests For|  Init  .Py / Mcmc Statistical Tests For]]
- [[_COMMUNITY_Init  .Py  Api Compatibility Tests Fo|  Init  .Py / Api Compatibility Tests Fo]]
- [[_COMMUNITY_Init  .Py  Performance And Benchmark|  Init  .Py / Performance And Benchmark ]]
- [[_COMMUNITY_Centralized Parameter Manager  Registry|Centralized Parameter Manager / Registry]]
- [[_COMMUNITY_Homodyne Model  Anomalous Diffusion Coe|Homodyne Model / Anomalous Diffusion Coe]]
- [[_COMMUNITY_Testrealdatastratification  Anti-Degene|Testrealdatastratification / Anti-Degene]]
- [[_COMMUNITY_Two-Time Correlation  Numerical Integra|Two-Time Correlation / Numerical Integra]]
- [[_COMMUNITY_Cli Quick Start  Configuration System|Cli Quick Start / Configuration System]]
- [[_COMMUNITY_Key Features  Consensus Monte Carlo|Key Features / Consensus Monte Carlo]]
- [[_COMMUNITY_Diffusionmodel  TAlpha Singularity|Diffusionmodel / T^Alpha Singularity]]
- [[_COMMUNITY_Diagonal Correction  Apply Diagonal Cor|Diagonal Correction / Apply Diagonal Cor]]
- [[_COMMUNITY_Docs Build Requirements  Sphinx + Furo|Docs Build Requirements / Sphinx + Furo ]]
- [[_COMMUNITY_Smooth Bounded Transform|Smooth Bounded Transform]]
- [[_COMMUNITY_Mcmc-Safe D0 Adjustment|Mcmc-Safe D0 Adjustment]]
- [[_COMMUNITY_Version.Py| Version.Py]]
- [[_COMMUNITY_Create Physicsfactors From Experimental|Create Physicsfactors From Experimental ]]
- [[_COMMUNITY_Compute G1 Correlation Function For This|Compute G1 Correlation Function For This]]
- [[_COMMUNITY_Get Parameter Bounds For Optimization.|Get Parameter Bounds For Optimization.]]
- [[_COMMUNITY_Get Default Parameter Values.|Get Default Parameter Values.]]
- [[_COMMUNITY_Compute Diffusion Contribution To G1.|Compute Diffusion Contribution To G1.   ]]
- [[_COMMUNITY_Compute Shear Contribution To G1.|Compute Shear Contribution To G1.       ]]
- [[_COMMUNITY_Compute Total G1 = G1 Diffusion × G1 She|Compute Total G1 = G1 Diffusion × G1 She]]
- [[_COMMUNITY_Compute G2 With Scaled Fitting G₂ = Off|Compute G2 With Scaled Fitting: G₂ = Off]]
- [[_COMMUNITY_Compute Chi-Squared Goodness Of Fit.|Compute Chi-Squared Goodness Of Fit.]]
- [[_COMMUNITY_Compute G1 Correlation Function.|Compute G1 Correlation Function.        ]]
- [[_COMMUNITY_Compute G2 With Scaled Fitting G₂ = Off|Compute G2 With Scaled Fitting: G₂ = Off]]
- [[_COMMUNITY_Compute Chi-Squared Goodness Of Fit.|Compute Chi-Squared Goodness Of Fit.    ]]
- [[_COMMUNITY_Compute Chi-Squared For Multiple Paramet|Compute Chi-Squared For Multiple Paramet]]
- [[_COMMUNITY_Get Configuration Summary For LoggingDe|Get Configuration Summary For Logging/De]]
- [[_COMMUNITY_Categorize Dataset Size.|Categorize Dataset Size.]]
- [[_COMMUNITY_Estimate Contrast And Offset Using Pure|Estimate Contrast And Offset Using Pure ]]
- [[_COMMUNITY_Compute Negative Log-Likelihood For Unif|Compute Negative Log-Likelihood For Unif]]
- [[_COMMUNITY_Load Parameterspace From Configuration D|Load Parameterspace From Configuration D]]
- [[_COMMUNITY_Create Parameterspace With Package Defau|Create Parameterspace With Package Defau]]
- [[_COMMUNITY_Base Names Of All Scaling Parameters (De|Base Names Of All Scaling Parameters (De]]
- [[_COMMUNITY_Create Cmcconfig From Configuration Dict|Create Cmcconfig From Configuration Dict]]
- [[_COMMUNITY_Return Ordered Values As Numpy Array.|Return Ordered Values As Numpy Array.]]
- [[_COMMUNITY_Return True If Sampling Converged (Backw|Return True If Sampling Converged (Backw]]
- [[_COMMUNITY_Return Descriptive Message About Result.|Return Descriptive Message About Result.]]
- [[_COMMUNITY_Create Cmcresult From Mcmc Samples.|Create Cmcresult From Mcmc Samples.     ]]
- [[_COMMUNITY_Backward-Compatible Alias For Enable D R|Backward-Compatible Alias For Enable D R]]
- [[_COMMUNITY_Backward-Compatible Alias For Enable Gam|Backward-Compatible Alias For Enable Gam]]
- [[_COMMUNITY_Number Of Worker Processes.|Number Of Worker Processes.]]
- [[_COMMUNITY_The Shared Result Queue Drained By The P|The Shared Result Queue Drained By The P]]
- [[_COMMUNITY_Run Mcmc Sampling (Potentially Across Sh|Run Mcmc Sampling (Potentially Across Sh]]
- [[_COMMUNITY_Check If Fourier Reparameterization Is A|Check If Fourier Reparameterization Is A]]
- [[_COMMUNITY_Get Number Of Parameters Per Group (Cont|Get Number Of Parameters Per Group (Cont]]
- [[_COMMUNITY_Get Human-Readable Name Of Current Mode.|Get Human-Readable Name Of Current Mode.]]
- [[_COMMUNITY_Get Total Number Of Per-Angle Parameters|Get Total Number Of Per-Angle Parameters]]
- [[_COMMUNITY_Get Total Number Of Parameters.|Get Total Number Of Parameters.]]
- [[_COMMUNITY_Get Physical Parameter Names For A Given|Get Physical Parameter Names For A Given]]
- [[_COMMUNITY_Return Nlsq-Specific Settings From The C|Return Nlsq-Specific Settings From The C]]
- [[_COMMUNITY_Normalize Nlsq Return Values To Consiste|Normalize Nlsq Return Values To Consiste]]
- [[_COMMUNITY_Create Nlsqconfig From Configuration Dic|Create Nlsqconfig From Configuration Dic]]
- [[_COMMUNITY_Create Nlsqconfig From Yaml Configuratio|Create Nlsqconfig From Yaml Configuratio]]
- [[_COMMUNITY_Create Cmaeswrapperconfig From Nlsqconfi|Create Cmaeswrapperconfig From Nlsqconfi]]
- [[_COMMUNITY_Check If Cma-Es Is Available.|Check If Cma-Es Is Available.]]
- [[_COMMUNITY_Return True If Optimization Converged (B|Return True If Optimization Converged (B]]
- [[_COMMUNITY_Return Descriptive Message About Optimiz|Return Descriptive Message About Optimiz]]
- [[_COMMUNITY_Create Config From Dictionary.|Create Config From Dictionary.]]
- [[_COMMUNITY_Get The Fourier Order (Number Of Harmoni|Get The Fourier Order (Number Of Harmoni]]
- [[_COMMUNITY_Create Config From Dictionary With Safe|Create Config From Dictionary With Safe ]]
- [[_COMMUNITY_Get Physical Parameter Names For A Given|Get Physical Parameter Names For A Given]]
- [[_COMMUNITY_Extract Nlsq-Specific Settings From Conf|Extract Nlsq-Specific Settings From Conf]]
- [[_COMMUNITY_Get Attribute From Dict Or Object.|Get Attribute From Dict Or Object.]]
- [[_COMMUNITY_Check If Nlsq Workflowselector Is Availa|Check If Nlsq Workflowselector Is Availa]]
- [[_COMMUNITY_Create Config From Nested Dictionary.|Create Config From Nested Dictionary.   ]]
- [[_COMMUNITY_Create Controller From Configuration Dic|Create Controller From Configuration Dic]]
- [[_COMMUNITY_Check If The Defense System Is Enabled A|Check If The Defense System Is Enabled A]]
- [[_COMMUNITY_Check If Fourier Reparameterization Is A|Check If Fourier Reparameterization Is A]]
- [[_COMMUNITY_Check If Constant Scaling Mode Is Active|Check If Constant Scaling Mode Is Active]]
- [[_COMMUNITY_Check If Using Fixed Per-Angle Scaling (|Check If Using Fixed Per-Angle Scaling (]]
- [[_COMMUNITY_Check If Using Optimized Averaged Scalin|Check If Using Optimized Averaged Scalin]]
- [[_COMMUNITY_Check If Hierarchical Optimization Is Ac|Check If Hierarchical Optimization Is Ac]]
- [[_COMMUNITY_Check If Shear-Sensitivity Weighting Is|Check If Shear-Sensitivity Weighting Is ]]
- [[_COMMUNITY_Get The Number Of Per-Angle Parameters (|Get The Number Of Per-Angle Parameters (]]
- [[_COMMUNITY_Create From Configuration Dictionary.|Create From Configuration Dictionary.   ]]
- [[_COMMUNITY_Current Phi0 Estimate In Degrees.|Current Phi0 Estimate In Degrees.]]
- [[_COMMUNITY_Create Multistartconfig From Nlsqconfig.|Create Multistartconfig From Nlsqconfig.]]
- [[_COMMUNITY_Create Config From Dictionary With Safe|Create Config From Dictionary With Safe ]]
- [[_COMMUNITY_Create Config From Dictionary With Safe|Create Config From Dictionary With Safe ]]
- [[_COMMUNITY_Create Progressconfig From Nlsqconfig.|Create Progressconfig From Nlsqconfig.  ]]
- [[_COMMUNITY_Fit The Model To Data.          Must Be|Fit The Model To Data.          Must Be ]]
- [[_COMMUNITY_Execute Optimization With The Specific S|Execute Optimization With The Specific S]]
- [[_COMMUNITY_Strategy Name For Logging.|Strategy Name For Logging.]]
- [[_COMMUNITY_Whether This Strategy Supports Progress|Whether This Strategy Supports Progress ]]
- [[_COMMUNITY_Create Fitqualityconfig From An Nlsqvali|Create Fitqualityconfig From An Nlsqvali]]
- [[_COMMUNITY_Get List Of Validation Errors From Last|Get List Of Validation Errors From Last ]]
- [[_COMMUNITY_Get List Of Validation Warnings From Las|Get List Of Validation Warnings From Las]]
- [[_COMMUNITY_Create Configuration From Dictionary.|Create Configuration From Dictionary.   ]]
- [[_COMMUNITY_Create Configuration From Cli Flags.|Create Configuration From Cli Flags.    ]]
- [[_COMMUNITY_Get Cache Hit Rate For This Pool.|Get Cache Hit Rate For This Pool.]]
- [[_COMMUNITY_Get Memory Usage Of This Pool In Mb.|Get Memory Usage Of This Pool In Mb.]]
- [[_COMMUNITY_Initialize Advanced Memory Manager.|Initialize Advanced Memory Manager.     ]]
- [[_COMMUNITY_Context Manager For Managed Memory Alloc|Context Manager For Managed Memory Alloc]]
- [[_COMMUNITY_Optimize Data Processing Specifically Fo|Optimize Data Processing Specifically Fo]]
- [[_COMMUNITY_Optimize Data Processing Specifically Fo|Optimize Data Processing Specifically Fo]]
- [[_COMMUNITY_Optimize Processing For Massive Datasets|Optimize Processing For Massive Datasets]]
- [[_COMMUNITY_Apply Comprehensive Filtering To Xpcs Da|Apply Comprehensive Filtering To Xpcs Da]]
- [[_COMMUNITY_Initialize Xpcs Data Loader With Yaml-Fi|Initialize Xpcs Data Loader With Yaml-Fi]]
- [[_COMMUNITY_Load Experimental Data With Priority Ca|Load Experimental Data With Priority: Ca]]
- [[_COMMUNITY_Load Data From Npz Cache File With Q-Vec|Load Data From Npz Cache File With Q-Vec]]
- [[_COMMUNITY_Load And Process Data From Hdf5 File.|Load And Process Data From Hdf5 File.]]
- [[_COMMUNITY_Detect Whether Hdf5 File Is Aps Old Or A|Detect Whether Hdf5 File Is Aps Old Or A]]
- [[_COMMUNITY_Load Data From Aps Old Format Hdf5 File.|Load Data From Aps Old Format Hdf5 File.]]
- [[_COMMUNITY_Load Data From Aps-U New Format Hdf5 Fil|Load Data From Aps-U New Format Hdf5 Fil]]
- [[_COMMUNITY_Save Processed Data To Npz Cache File Wi|Save Processed Data To Npz Cache File Wi]]
- [[_COMMUNITY_Save Phi Angles And Wavevector Q Lists T|Save Phi Angles And Wavevector Q Lists T]]
- [[_COMMUNITY_Apply Preprocessing Pipeline To Loaded D|Apply Preprocessing Pipeline To Loaded D]]
- [[_COMMUNITY_Context Manager For Memory-Mapped Hdf5 F|Context Manager For Memory-Mapped Hdf5 F]]
- [[_COMMUNITY_Initialize Performance Engine With Confi|Initialize Performance Engine With Confi]]
- [[_COMMUNITY_Load Correlation Matrices With Full Perf|Load Correlation Matrices With Full Perf]]
- [[_COMMUNITY_Initialize Preprocessing Pipeline With C|Initialize Preprocessing Pipeline With C]]
- [[_COMMUNITY_Execute The Full Preprocessing Pipeline|Execute The Full Preprocessing Pipeline ]]
- [[_COMMUNITY_Enhanced Diagonal Correction With Multip|Enhanced Diagonal Correction With Multip]]
- [[_COMMUNITY_Apply Normalization To Correlation Data|Apply Normalization To Correlation Data ]]
- [[_COMMUNITY_Apply Noise Reduction Algorithms To Corr|Apply Noise Reduction Algorithms To Corr]]
- [[_COMMUNITY_Create Configuration From Dictionary.|Create Configuration From Dictionary.]]
- [[_COMMUNITY_Validate Data At Specific Pipeline Stage|Validate Data At Specific Pipeline Stage]]
- [[_COMMUNITY_Validate Raw Data Integrity And Basic Fo|Validate Raw Data Integrity And Basic Fo]]
- [[_COMMUNITY_Apply Automatic Data Repair Based On Det|Apply Automatic Data Repair Based On Det]]
- [[_COMMUNITY_Generate Comprehensive Quality Assessmen|Generate Comprehensive Quality Assessmen]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Get Path To Docs Directory.|Get Path To Docs Directory.]]
- [[_COMMUNITY_Verify Sigma Override Is Applied In To C|Verify Sigma Override Is Applied In To C]]
- [[_COMMUNITY_When Warmstart Chi2 Is Provided, Cma-Es|When Warmstart Chi2 Is Provided, Cma-Es ]]
- [[_COMMUNITY_Without Warmstart Chi2, Cma-Es Should Us|Without Warmstart Chi2, Cma-Es Should Us]]
- [[_COMMUNITY_Test Yaml Configuration File Loading.|Test Yaml Configuration File Loading.]]
- [[_COMMUNITY_Small Set Of Phi Angles ( Threshold).|Small Set Of Phi Angles (< Threshold).]]
- [[_COMMUNITY_Large Set Of Phi Angles ( Threshold).|Large Set Of Phi Angles (> Threshold).]]
- [[_COMMUNITY_Create A Simple Hierarchical Optimizer.|Create A Simple Hierarchical Optimizer.]]
- [[_COMMUNITY_Create A Regularizer For Testing.|Create A Regularizer For Testing.]]
- [[_COMMUNITY_Create A Monitor For Testing.|Create A Monitor For Testing.]]
- [[_COMMUNITY_Create Synthetic 23-Angle Laminar Flow D|Create Synthetic 23-Angle Laminar Flow D]]
- [[_COMMUNITY_Create Controller For 23-Angle Laminar F|Create Controller For 23-Angle Laminar F]]
- [[_COMMUNITY_Create Controller For 5-Angle (Below Fou|Create Controller For 5-Angle (Below Fou]]
- [[_COMMUNITY_Check If Jax Is Available.|Check If Jax Is Available.]]
- [[_COMMUNITY_Create Simple Stratified Data For Testin|Create Simple Stratified Data For Testin]]
- [[_COMMUNITY_Create Stratified Data With Multiple Ang|Create Stratified Data With Multiple Ang]]
- [[_COMMUNITY_Test Nlsq Fitting With Synthetic Data.|Test Nlsq Fitting With Synthetic Data.  ]]
- [[_COMMUNITY_Test Parameter Recovery With Known Synth|Test Parameter Recovery With Known Synth]]
- [[_COMMUNITY_Test Nlsq Optimization With Boundary Con|Test Nlsq Optimization With Boundary Con]]
- [[_COMMUNITY_Test Nlsq Optimization With Shear Flow.|Test Nlsq Optimization With Shear Flow.]]
- [[_COMMUNITY_Test Nlsq Optimization With Multiple Q-V|Test Nlsq Optimization With Multiple Q-V]]
- [[_COMMUNITY_Validation Should Handle Jax Tracers Gra|Validation Should Handle Jax Tracers Gra]]
- [[_COMMUNITY_Test Explicit Jax Backend Selection.|Test Explicit Jax Backend Selection.]]
- [[_COMMUNITY_Test Auto Backend Detection With Jax Inp|Test Auto Backend Detection With Jax Inp]]
- [[_COMMUNITY_Test Batch Processing With Jax Backend.|Test Batch Processing With Jax Backend.]]
- [[_COMMUNITY_Property Applying Correction Twice Shou|Property: Applying Correction Twice Shou]]
- [[_COMMUNITY_Property Off-Diagonal Elements Must Be|Property: Off-Diagonal Elements Must Be ]]
- [[_COMMUNITY_Property Uniform Matrix Diagonal Should|Property: Uniform Matrix Diagonal Should]]
- [[_COMMUNITY_Test That G1 Diffusion Decreases With In|Test That G1 Diffusion Decreases With In]]
- [[_COMMUNITY_Test C2 Model Scaling Properties.|Test C2 Model Scaling Properties.]]
- [[_COMMUNITY_Test That Residuals Have Zero Mean For P|Test That Residuals Have Zero Mean For P]]
- [[_COMMUNITY_Standard Diffusion Parameters For Testin|Standard Diffusion Parameters For Testin]]
- [[_COMMUNITY_Standard Shear Parameters For Testing.|Standard Shear Parameters For Testing.]]
- [[_COMMUNITY_Full 7-Parameter Set For Combined Diffus|Full 7-Parameter Set For Combined Diffus]]
- [[_COMMUNITY_Standard Diffusion Parameters For Perfor|Standard Diffusion Parameters For Perfor]]
- [[_COMMUNITY_Test Loading Data With --Data-File Cli O|Test Loading Data With --Data-File Cli O]]
- [[_COMMUNITY_Test Loading Data From Configuration Fil|Test Loading Data From Configuration Fil]]
- [[_COMMUNITY_Test Loading Data With Relative Path (Ed|Test Loading Data With Relative Path (Ed]]
- [[_COMMUNITY_Test Error Handling When Data File Doesn|Test Error Handling When Data File Doesn]]
- [[_COMMUNITY_Test Loading Data With Complex Path (Spa|Test Loading Data With Complex Path (Spa]]
- [[_COMMUNITY_Test --Cmc-Num-Shards Cli Argument Overr|Test --Cmc-Num-Shards Cli Argument Overr]]
- [[_COMMUNITY_Test --Cmc-Backend Cli Argument Override|Test --Cmc-Backend Cli Argument Override]]
- [[_COMMUNITY_Test Diagnostic Plots Are Generated When|Test Diagnostic Plots Are Generated When]]
- [[_COMMUNITY_Test Diagnostic Plots Are Not Generated|Test Diagnostic Plots Are Not Generated ]]
- [[_COMMUNITY_Test Diagnostic Plots Are Always Generat|Test Diagnostic Plots Are Always Generat]]
- [[_COMMUNITY_Test  Generate Cmc Diagnostic Plots Gene|Test  Generate Cmc Diagnostic Plots Gene]]
- [[_COMMUNITY_Test  Generate Cmc Diagnostic Plots Work|Test  Generate Cmc Diagnostic Plots Work]]
- [[_COMMUNITY_Create A Mock Optimization Result.|Create A Mock Optimization Result.]]
- [[_COMMUNITY_Create Mock Experimental Data.|Create Mock Experimental Data.]]
- [[_COMMUNITY_Create Mock Metadata.|Create Mock Metadata.]]
- [[_COMMUNITY_Ensure Nlsq Components Are Available For|Ensure Nlsq Components Are Available For]]
- [[_COMMUNITY_Should Fallback To Os.Sysconf When Psuti|Should Fallback To Os.Sysconf When Psuti]]
- [[_COMMUNITY_Verify Memory Estimation Formula Against|Verify Memory Estimation Formula Against]]
- [[_COMMUNITY_Test Strategy Selection Across Various D|Test Strategy Selection Across Various D]]
- [[_COMMUNITY_Nlsqwrapper Should Be Importable.|Nlsqwrapper Should Be Importable.]]
- [[_COMMUNITY_Nlsqwrapper Should Accept Enable Recover|Nlsqwrapper Should Accept Enable Recover]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Concrete Adapter For Testing.|Create A Concrete Adapter For Testing.]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Create Minimal Valid Xpcs Data.|Create Minimal Valid Xpcs Data.]]
- [[_COMMUNITY_Create Minimal Valid Xpcs Data.|Create Minimal Valid Xpcs Data.]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Empty Hdf5 File Should Return 'Unknown'|Empty Hdf5 File Should Return 'Unknown' ]]
- [[_COMMUNITY_Aps-U Format Structure Should Be Detecte|Aps-U Format Structure Should Be Detecte]]
- [[_COMMUNITY_Aps Old Format Structure Should Be Detec|Aps Old Format Structure Should Be Detec]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Create A Mock Loader For Testing Interna|Create A Mock Loader For Testing Interna]]
- [[_COMMUNITY_Verify Jacobian Memory Calculation.|Verify Jacobian Memory Calculation.]]
- [[_COMMUNITY_Test That Cpu Functions Are Exported Whe|Test That Cpu Functions Are Exported Whe]]
- [[_COMMUNITY_Test With Synthetic 100M Point Dataset.|Test With Synthetic 100M Point Dataset.]]
- [[_COMMUNITY_Test Safe Len With 1D Jax Array.|Test Safe Len With 1D Jax Array.]]
- [[_COMMUNITY_Test Safe Len With 2D Jax Array.|Test Safe Len With 2D Jax Array.]]
- [[_COMMUNITY_Test Safe Len With Jax Scalar.|Test Safe Len With Jax Scalar.]]
- [[_COMMUNITY_Standard Phi Angles For Testing.|Standard Phi Angles For Testing.]]
- [[_COMMUNITY_Create A Weighter Instance For Testing.|Create A Weighter Instance For Testing.]]
- [[_COMMUNITY_Test That Parameter Count Scales Correct|Test That Parameter Count Scales Correct]]
- [[_COMMUNITY_Create A Sample Cmcresult For Testing.|Create A Sample Cmcresult For Testing.]]
- [[_COMMUNITY_Create Result With Real Sample Structure|Create Result With Real Sample Structure]]
- [[_COMMUNITY_Create A Complete Static Result For Vali|Create A Complete Static Result For Vali]]
- [[_COMMUNITY_Create Multi-Angle Prepared Data For Tes|Create Multi-Angle Prepared Data For Tes]]
- [[_COMMUNITY_Create Laminar Flow Parameter Space.|Create Laminar Flow Parameter Space.]]
- [[_COMMUNITY_Create Static Parameter Space.|Create Static Parameter Space.]]
- [[_COMMUNITY_Create Sample Scalings For Testing.|Create Sample Scalings For Testing.]]
- [[_COMMUNITY_Create Sample Scalings For Testing.|Create Sample Scalings For Testing.]]
- [[_COMMUNITY_Create A Mock Parameterspace For Testing|Create A Mock Parameterspace For Testing]]
- [[_COMMUNITY_Create A Mock Parameterspace For Testing|Create A Mock Parameterspace For Testing]]
- [[_COMMUNITY_Create A Mock Parameterspace For Testing|Create A Mock Parameterspace For Testing]]
- [[_COMMUNITY_Create A Mock Parameterspace For Testing|Create A Mock Parameterspace For Testing]]
- [[_COMMUNITY_Standard Test Parameters.|Standard Test Parameters.]]
- [[_COMMUNITY_Create A Minimal Parameter Space For Tes|Create A Minimal Parameter Space For Tes]]
- [[_COMMUNITY_Create Mock Cmcresult For Testing.|Create Mock Cmcresult For Testing.]]
- [[_COMMUNITY_Create Mock Result With Known Values.|Create Mock Result With Known Values.]]
- [[_COMMUNITY_Create A Mock Parameter Space For Testin|Create A Mock Parameter Space For Testin]]
- [[_COMMUNITY_Test That Combining Preserves Sample Sha|Test That Combining Preserves Sample Sha]]
- [[_COMMUNITY_Test That All Combination Methods Produc|Test That All Combination Methods Produc]]
- [[_COMMUNITY_Test That Legacy Combination Methods Wor|Test That Legacy Combination Methods Wor]]
- [[_COMMUNITY_Create A Minimal Parameterspace For Test|Create A Minimal Parameterspace For Test]]
- [[_COMMUNITY_Test That Sample Shapes Are Always (N Ch|Test That Sample Shapes Are Always (N Ch]]
- [[_COMMUNITY_Create A Mock Scaling Dict With .Scale A|Create A Mock Scaling Dict With .Scale A]]
- [[_COMMUNITY_Standard Laminar Flow Test Parameters.|Standard Laminar Flow Test Parameters.]]
- [[_COMMUNITY_Standard Static Test Parameters (3 Param|Standard Static Test Parameters (3 Param]]
- [[_COMMUNITY_Test Phi Angles (Degrees).|Test Phi Angles (Degrees).]]
- [[_COMMUNITY_Init  .Py|  Init  .Py]]
- [[_COMMUNITY_Init  .Py|  Init  .Py]]
- [[_COMMUNITY_Test Workflow With Yaml Configuration.|Test Workflow With Yaml Configuration.]]
- [[_COMMUNITY_Verify Auto Mode Selects Auto Averaged F|Verify Auto Mode Selects Auto Averaged F]]
- [[_COMMUNITY_Verify 23-Angle Laminar Flow Uses 9 Para|Verify 23-Angle Laminar Flow Uses 9 Para]]
- [[_COMMUNITY_Test Initial Parameter Transformation Fr|Test Initial Parameter Transformation Fr]]
- [[_COMMUNITY_Verify Constant Mode Results Expand To P|Verify Constant Mode Results Expand To P]]
- [[_COMMUNITY_Verify Diagnostics Include Constant Mode|Verify Diagnostics Include Constant Mode]]
- [[_COMMUNITY_Worker Function That Runs In A Separate|Worker Function That Runs In A Separate ]]
- [[_COMMUNITY_Verify Optimizer Completes Without Index|Verify Optimizer Completes Without Index]]
- [[_COMMUNITY_Verify Gamma Dot T0  1E-04 After Optimi|Verify Gamma Dot T0 > 1E-04 After Optimi]]
- [[_COMMUNITY_Verify Per-Angle ContrastOffset Cv  20|Verify Per-Angle Contrast/Offset Cv < 20]]
- [[_COMMUNITY_Verify Warning Logged When Group Indices|Verify Warning Logged When Group Indices]]
- [[_COMMUNITY_Verify Warning Logged When Hybrid Optimi|Verify Warning Logged When Hybrid Optimi]]
- [[_COMMUNITY_Verify Covariance Matrix Is Correctly Tr|Verify Covariance Matrix Is Correctly Tr]]
- [[_COMMUNITY_Verify Relative Uncertainty On Gamma Dot|Verify Relative Uncertainty On Gamma Dot]]
- [[_COMMUNITY_Verify 3-Phi Case Still Works Correctly.|Verify 3-Phi Case Still Works Correctly.]]
- [[_COMMUNITY_Generate Synthetic C2 Data For Testing P|Generate Synthetic C2 Data For Testing P]]
- [[_COMMUNITY_Test Handling Of 180 Angles × 100×100 Co|Test Handling Of 180 Angles × 100×100 Co]]
- [[_COMMUNITY_Test Full Cli Workflow From Config To Sa|Test Full Cli Workflow From Config To Sa]]
- [[_COMMUNITY_Reparameterized Model Produces Samples C|Reparameterized Model Produces Samples C]]
- [[_COMMUNITY_Verify Core.Py Forces Angle-Balanced Sha|Verify Core.Py Forces Angle-Balanced Sha]]
- [[_COMMUNITY_Verify Stratified Is Still Allowed For S|Verify Stratified Is Still Allowed For S]]
- [[_COMMUNITY_Init  .Py|  Init  .Py]]
- [[_COMMUNITY_Create Basic Configuration.|Create Basic Configuration.]]
- [[_COMMUNITY_Create Configuration Optimized For Perfo|Create Configuration Optimized For Perfo]]
- [[_COMMUNITY_Create Configuration For Mcmc Testing.|Create Configuration For Mcmc Testing.]]
- [[_COMMUNITY_Save Configuration To File.|Save Configuration To File.]]
- [[_COMMUNITY_Create Realistic Physical Parameters.|Create Realistic Physical Parameters.]]
- [[_COMMUNITY_Create Parameter Sweep For Testing.|Create Parameter Sweep For Testing.]]
- [[_COMMUNITY_Create Edge Case Parameter Sets.|Create Edge Case Parameter Sets.]]
- [[_COMMUNITY_E2E Test Recover Static Mode Parameters|E2E Test: Recover Static Mode Parameters]]
- [[_COMMUNITY_Load From Dictionary.|Load From Dictionary.]]
- [[_COMMUNITY_Init  .Py|  Init  .Py]]
- [[_COMMUNITY_Conf.Py|Conf.Py]]
- [[_COMMUNITY_Homodyne Package|Homodyne Package]]
- [[_COMMUNITY_Mcmc Preflight Diagnostics|Mcmc Preflight Diagnostics]]
- [[_COMMUNITY_Rate Functions|Rate Functions]]
- [[_COMMUNITY_Homodyne Parameters|Homodyne Parameters]]
- [[_COMMUNITY_Design Principles|Design Principles]]
- [[_COMMUNITY_Nuts Sampling|Nuts Sampling]]
- [[_COMMUNITY_Cma-Es Global Optimization|Cma-Es Global Optimization]]
- [[_COMMUNITY_Time-Dependent Shear Rate|Time-Dependent Shear Rate]]
- [[_COMMUNITY_Quality Control System|Quality Control System]]
- [[_COMMUNITY_Testscientificvalidation|Testscientificvalidation]]
- [[_COMMUNITY_Numerical Stability Test|Numerical Stability Test]]
- [[_COMMUNITY_Testasyncwriter|Testasyncwriter]]
- [[_COMMUNITY_How To Contribute|How To Contribute]]
- [[_COMMUNITY_Jax Cpu Backend|Jax Cpu Backend]]
- [[_COMMUNITY_Shardgrid|Shardgrid]]
- [[_COMMUNITY_Compute G1 Total With Precomputed|Compute G1 Total With Precomputed]]
- [[_COMMUNITY_Compute G1 Diffusion|Compute G1 Diffusion]]
- [[_COMMUNITY_Compute G1 Total|Compute G1 Total]]
- [[_COMMUNITY_Physicsfactors|Physicsfactors]]
- [[_COMMUNITY_Create Physics Factors From Config Dict|Create Physics Factors From Config Dict]]
- [[_COMMUNITY_Physicsmodelprotocol| Physicsmodelprotocol]]
- [[_COMMUNITY_Gradientcapabilitymixin|Gradientcapabilitymixin]]
- [[_COMMUNITY_Benchmarkingmixin|Benchmarkingmixin]]
- [[_COMMUNITY_Optimizationrecommendationmixin|Optimizationrecommendationmixin]]
- [[_COMMUNITY_Estimate Contrast Offset From Quantiles|Estimate Contrast Offset From Quantiles]]
- [[_COMMUNITY_Compute Averaged Scaling|Compute Averaged Scaling]]
- [[_COMMUNITY_Apply Diagonal Correction Batch|Apply Diagonal Correction Batch]]
- [[_COMMUNITY_Get Diagonal Correction Methods|Get Diagonal Correction Methods]]
- [[_COMMUNITY_Get Available Backends|Get Available Backends]]
- [[_COMMUNITY_Physicsmodelbase|Physicsmodelbase]]
- [[_COMMUNITY_Shearmodel|Shearmodel]]
- [[_COMMUNITY_Combinedmodel|Combinedmodel]]
- [[_COMMUNITY_Create Model|Create Model]]
- [[_COMMUNITY_Get Available Models|Get Available Models]]
- [[_COMMUNITY_Compute G2 Scaled|Compute G2 Scaled]]
- [[_COMMUNITY_Compute G2 Scaled With Factors|Compute G2 Scaled With Factors]]
- [[_COMMUNITY_Differentiationmethod|Differentiationmethod]]
- [[_COMMUNITY_Differentiationconfig|Differentiationconfig]]
- [[_COMMUNITY_Gradientresult|Gradientresult]]
- [[_COMMUNITY_Numericalstabilityerror|Numericalstabilityerror]]
- [[_COMMUNITY_Numpy Gradient|Numpy Gradient]]
- [[_COMMUNITY_Numpy Hessian|Numpy Hessian]]
- [[_COMMUNITY_Validate Gradient Accuracy|Validate Gradient Accuracy]]
- [[_COMMUNITY_Theoryengine|Theoryengine]]
- [[_COMMUNITY_Compute G2 Theory|Compute G2 Theory]]
- [[_COMMUNITY_Compute Chi2 Theory|Compute Chi2 Theory]]
- [[_COMMUNITY_Validationresult|Validationresult]]
- [[_COMMUNITY_Physicsconstants|Physicsconstants]]
- [[_COMMUNITY_Parameter Bounds|Parameter Bounds]]
- [[_COMMUNITY_Validate Parameters Detailed|Validate Parameters Detailed]]
- [[_COMMUNITY_Validate Parameters|Validate Parameters]]
- [[_COMMUNITY_Clip Parameters|Clip Parameters]]
- [[_COMMUNITY_Get Default Parameters|Get Default Parameters]]
- [[_COMMUNITY_Validate Experimental Setup|Validate Experimental Setup]]
- [[_COMMUNITY_Estimate Correlation Time|Estimate Correlation Time]]
- [[_COMMUNITY_Get Parameter Info|Get Parameter Info]]
- [[_COMMUNITY_Homodynemodel|Homodynemodel]]
- [[_COMMUNITY_Parameterspace|Parameterspace]]
- [[_COMMUNITY_Datasetsize|Datasetsize]]
- [[_COMMUNITY_Fitresult|Fitresult]]
- [[_COMMUNITY_Unifiedhomodyneengine|Unifiedhomodyneengine]]
- [[_COMMUNITY_Get Cached Meshgrid|Get Cached Meshgrid]]
- [[_COMMUNITY_Clear Meshgrid Cache|Clear Meshgrid Cache]]
- [[_COMMUNITY_Get Cache Stats|Get Cache Stats]]
- [[_COMMUNITY_Reset Cache Stats|Reset Cache Stats]]
- [[_COMMUNITY_Compute G1 Diffusion|Compute G1 Diffusion]]
- [[_COMMUNITY_Compute G1 Shear|Compute G1 Shear]]
- [[_COMMUNITY_Compute G1 Total|Compute G1 Total]]
- [[_COMMUNITY_Compute G2 Scaled|Compute G2 Scaled]]
- [[_COMMUNITY_Compute G2 Scaled With Factors|Compute G2 Scaled With Factors]]
- [[_COMMUNITY_Compute Chi Squared|Compute Chi Squared]]
- [[_COMMUNITY_Vectorized G2 Computation|Vectorized G2 Computation]]
- [[_COMMUNITY_Batch Chi Squared|Batch Chi Squared]]
- [[_COMMUNITY_Validate Backend|Validate Backend]]
- [[_COMMUNITY_Get Device Info|Get Device Info]]
- [[_COMMUNITY_Get Performance Summary|Get Performance Summary]]
- [[_COMMUNITY_Safe Len|Safe Len]]
- [[_COMMUNITY_Safe Exp|Safe Exp]]
- [[_COMMUNITY_Safe Sinc|Safe Sinc]]
- [[_COMMUNITY_Calculate Diffusion Coefficient|Calculate Diffusion Coefficient]]
- [[_COMMUNITY_Calculate Shear Rate|Calculate Shear Rate]]
- [[_COMMUNITY_Calculate Shear Rate Cmc|Calculate Shear Rate Cmc]]
- [[_COMMUNITY_Create Time Integral Matrix|Create Time Integral Matrix]]
- [[_COMMUNITY_Trapezoid Cumsum|Trapezoid Cumsum]]
- [[_COMMUNITY_Parametermanager|Parametermanager]]
- [[_COMMUNITY_Bounddict|Bounddict]]
- [[_COMMUNITY_Initialparametersconfig|Initialparametersconfig]]
- [[_COMMUNITY_Parameterspaceconfig|Parameterspaceconfig]]
- [[_COMMUNITY_Experimentaldataconfig|Experimentaldataconfig]]
- [[_COMMUNITY_Streamingconfig|Streamingconfig]]
- [[_COMMUNITY_Stratificationconfig|Stratificationconfig]]
- [[_COMMUNITY_Sequentialconfig|Sequentialconfig]]
- [[_COMMUNITY_Cmcshardingconfig|Cmcshardingconfig]]
- [[_COMMUNITY_Cmcinitializationconfig|Cmcinitializationconfig]]
- [[_COMMUNITY_Cmcbackendconfig|Cmcbackendconfig]]
- [[_COMMUNITY_Cmccombinationconfig|Cmccombinationconfig]]
- [[_COMMUNITY_Cmcpershardmcmcconfig|Cmcpershardmcmcconfig]]
- [[_COMMUNITY_Nlsqvalidationconfig|Nlsqvalidationconfig]]
- [[_COMMUNITY_Cmcvalidationconfig|Cmcvalidationconfig]]
- [[_COMMUNITY_Cmcconfig|Cmcconfig]]
- [[_COMMUNITY_Optimizationconfig|Optimizationconfig]]
- [[_COMMUNITY_Homodyneconfig|Homodyneconfig]]
- [[_COMMUNITY_Get Parameter Names|Get Parameter Names]]
- [[_COMMUNITY_Get Physical Param Names|Get Physical Param Names]]
- [[_COMMUNITY_Get Num Parameters|Get Num Parameters]]
- [[_COMMUNITY_Verify Samples Dict|Verify Samples Dict]]
- [[_COMMUNITY_Furo-Extensions.Js|Furo-Extensions.Js]]
- [[_COMMUNITY_Furo-Extensions.Js|Furo-Extensions.Js]]
- [[_COMMUNITY_Backward-Compatible Alias For Enable D R|Backward-Compatible Alias For Enable D R]]
- [[_COMMUNITY_Backward-Compatible Alias For Enable Gam|Backward-Compatible Alias For Enable Gam]]
- [[_COMMUNITY_Api Utilities|Api: Utilities]]
- [[_COMMUNITY_Cmc Time Grid Construction|Cmc Time Grid Construction]]
- [[_COMMUNITY_Physicsconstants|Physicsconstants]]
- [[_COMMUNITY_DeviceCpu.Py (Cpu Topology Detection)|Device/Cpu.Py (Cpu Topology Detection)]]
- [[_COMMUNITY_Examples Index|Examples Index]]
- [[_COMMUNITY_Glossary Term Homodyne Detection (No Re|Glossary Term: Homodyne Detection (No Re]]
- [[_COMMUNITY_Community 1048|Community 1048]]
- [[_COMMUNITY_Community 1049|Community 1049]]

## God Nodes (most connected - your core abstractions)
1. `ConfigManager` - 227 edges
2. `NLSQWrapper` - 184 edges
3. `ParameterManager` - 182 edges
4. `CMCConfig` - 114 edges
5. `XPCSDataLoader` - 100 edges
6. `MCMCSamples` - 97 edges
7. `AntiDegeneracyController` - 95 edges
8. `ParameterSpace` - 79 edges
9. `CheckpointManager` - 79 edges
10. `AntiDegeneracyConfig` - 72 edges

## Surprising Connections (you probably didn't know these)
- `fit_mcmc_jax() Function` --calls--> `CMC data_prep.py (sharding, validation, noise estimation)`  [INFERRED]
  docs/architecture/cmc-fitting-architecture.md → homodyne/optimization/cmc/data_prep.py
- `CMC MultiprocessingBackend` --calls--> `SamplingPlan`  [INFERRED]
  docs/architecture/cmc-fitting-architecture.md → homodyne/optimization/cmc/sampler.py
- `CMC MultiprocessingBackend` --shares_data_with--> `DeviceConfig (n_workers, threads, memory, avx512)`  [INFERRED]
  docs/architecture/cmc-fitting-architecture.md → homodyne/device/config.py
- `CombinedModel (3 or 7 params, primary)` --implements--> `Static Analysis Mode (3 params: D0, alpha, D_offset)`  [INFERRED]
  homodyne/core/models.py → docs/source/architecture/homodyne-architecture-overview.md
- `CombinedModel (3 or 7 params, primary)` --implements--> `Laminar Flow Analysis Mode (7 params)`  [INFERRED]
  homodyne/core/models.py → docs/source/architecture/homodyne-architecture-overview.md

## Hyperedges (group relationships)
- **NLSQ→CMC Warm-Start: NLSQ result feeds CMC priors, reducing divergences from 28% to <5%** — concept_nlsq_warmstart, concept_nlsq_wrapper, concept_cmc_config, concept_consensus_mc [EXTRACTED 0.95]
- **Shadow-Copy Architecture: 5 parallel g1/g2 implementations for NLSQ, CMC, dispatcher, element-wise, test reference** — concept_shadow_copy, concept_xpcs_g1g2, adr_shadow_copy, arch_physical [EXTRACTED 0.95]
- **Anti-Degeneracy Defense System: controller, per-angle scaling ADR, and NLSQ architecture together prevent parameter absorption** — concept_anti_degeneracy_ctrl, concept_anti_degeneracy, adr_per_angle_scaling [EXTRACTED 0.90]
- **CMC Execution Pipeline: Sharding + NUTS + Consensus** — shard_size_selection_concept, nuts_sampling_concept, consensus_mc_concept [EXTRACTED 1.00]
- **NLSQ-CMC Integration: Warm-Start + Prior Tempering + Informed Priors** — nlsq_warmstart_concept, prior_tempering_concept, reparameterization_concept [EXTRACTED 0.95]
- **Physics Numerical Stability: Log-Space + Gradient-Safe Floors + Safe Sinc** — log_space_computation_concept, gradient_safe_floor_concept, shadow_copy_architecture_concept [EXTRACTED 0.95]

## Communities (1050 total, 519 thin omitted)

### Community 0 - "Test Fixtures & Process Utilities"
Cohesion: 0.01
Nodes (157): LargeDatasetFactory, Create a generator for batch-wise data processing.          This generator yield, Factory for generating large-scale mock XPCS datasets., Initialize factory with deterministic random seed.          Parameters         -, generate_static_mode_dataset(), Generate static mode synthetic dataset with default parameters.      Generates p, Test with both static_mode and laminar_flow modes., Test full pipeline with LARGE strategy (1M - 10M points). (+149 more)

### Community 1 - "Result Serialization & Messaging"
Cohesion: 0.02
Nodes (173): Test stratification preserves all data points (no duplicates or losses)., test_stratification_preserves_all_data_points(), Marker indicating sequential per-angle optimization should be used.      This is, UseSequentialOptimization, Apply angle-stratified chunking if conditions require it.          This method f, AngleDistributionStats, compute_stratification_diagnostics(), create_angle_stratified_data() (+165 more)

### Community 2 - "JAX Backend & Config Toggles"
Cohesion: 0.01
Nodes (124): NumericalStabilityError, Raised when numerical differentiation encounters stability issues., _correct_diagonal_enhanced(), __init__(), PreprocessingPipeline, Advanced data preprocessing pipeline with configurable transformation stages., Validate preprocessing configuration parameters., Get list of enabled preprocessing stages based on configuration. (+116 more)

### Community 3 - "CMC Priors & Sampler Core"
Cohesion: 0.02
Nodes (111): _combine_shard_chunk(), combine_shard_samples(), combine_shard_samples_bimodal(), Base class for CMC execution backends.  This module defines the abstract interfa, # NOTE: Map to multiprocessing, not pjit, because pjit backend is sequential, Combine samples from multiple shards.      For K <= chunk_size shards, uses a si, Combine a chunk of shard samples (internal helper).      Parameters     --------, Combine shard samples using mode-aware consensus.      For bimodal shards, uses (+103 more)

### Community 4 - "Optimization Enums & Logging"
Cohesion: 0.04
Nodes (106): MockOptimizationResult, Integration tests for laminar flow optimization with many phi angles.  Tests the, Test that gamma_dot_t0 recovers to physical values (US1)., Test that per-angle parameters have low coefficient of variation (US1)., Test warning logged on configuration mismatch (US2)., Test warning logged when falling back to basic streaming (US2)., Test covariance transformation from Fourier to per-angle space (US3)., Test relative uncertainty bounds on gamma_dot_t0 (US3). (+98 more)

### Community 5 - "Checkpoint & Resume System"
Cohesion: 0.02
Nodes (82): Test checkpoint is saved during optimization., Test resuming optimization from checkpoint after interruption.          Scenario, Test automatic cleanup of old checkpoints., Test multiple interruption/resume cycles., Test automatic checkpoint cleanup keeps only recent checkpoints., test_checkpoint_manager_cleanup(), CheckpointManager, Checkpoint management for streaming optimization.  This module provides checkpoi (+74 more)

### Community 6 - "CMC Config & Runner"
Cohesion: 0.02
Nodes (89): MockOptimizationResult, Integration tests for constant scaling mode in NLSQ optimization.  Tests the end, T056: Test output NPZ compatibility with constant scaling., Mock optimization result for testing., T053: Test constant scaling auto-selection with realistic setup., T054-T055: Test parameter count reduction with constant scaling., test_auto_selects_constant_for_23_phi(), test_diagnostics_include_constant_mode_info() (+81 more)

### Community 7 - "NLSQ Memory & Strategy Tests"
Cohesion: 0.02
Nodes (75): ParameterIndexMapper, Centralized index mapping for anti-degeneracy layers.  This module provides the, Get (start, end) tuples for contrast and offset parameter groups.          Retur, Get indices of physical parameters.          Returns         -------         lis, Get indices of all per-angle parameters.          Returns         -------, Validate that group indices are within parameter vector bounds.          Paramet, Get diagnostic information for logging.          Returns         -------, Centralized index mapping for anti-degeneracy layers.      Provides consistent i (+67 more)

### Community 8 - "MCMC Diagnostics & Monitoring"
Cohesion: 0.02
Nodes (96): CMCBackend, Abstract base class for CMC execution backends.      Backends handle the paralle, Check if backend is available.          Returns         -------         bool, BimodalConsensusResult, BimodalResult, check_convergence(), check_shard_bimodality(), cluster_shard_modes() (+88 more)

### Community 9 - "Gradient & Regularizer Tests"
Cohesion: 0.03
Nodes (88): _exclude_t0_from_analysis(), Exclude t=0 (index 0) from time arrays and C2 data for analysis.      With anoma, PreparedData, Validated and prepared data for MCMC sampling.      Attributes     ----------, CMCResult, Return True - required by CLI for diagnostic generation., Get samples as 3D array.          Returns         -------         np.ndarray, Validate that result contains expected parameters.          Parameters         - (+80 more)

### Community 10 - "Data Structures & Base Classes"
Cohesion: 0.03
Nodes (67): AdaptiveChunker, CacheError, ChunkInfo, __init__(), load_correlation_matrices_optimized(), MemoryMapManager, MemoryPressureError, MultiLevelCache (+59 more)

### Community 11 - "Per-Angle Scaling Modes"
Cohesion: 0.03
Nodes (87): get_data_module_info(), Data Loading and Management for Homodyne =======================================, Get information about data module capabilities.      Returns:         Dictionary, XPCSConfigurationError, XPCSDataFormatError, XPCSDataLoader, XPCSDependencyError, create_advanced_dataset_optimizer() (+79 more)

### Community 12 - "CMC Backend & Bimodal Detection"
Cohesion: 0.03
Nodes (70): PhysicsConstants, Physical constants and reference values for XPCS analysis.      These values are, apply_data_filtering(), apply_filtering(), DataFilteringError, FilterCriteria, FilteringResult, Data Filtering Utilities for XPCS Data Loader ================================== (+62 more)

### Community 13 - "CMC Result & Sampling Plan"
Cohesion: 0.03
Nodes (69): Verify memory-based strategy selection for various dataset sizes., Small datasets (< 1M points) should use STANDARD strategy., StrategyDecision should expose all documented fields., Larger datasets must produce larger peak memory estimates., More parameters must produce larger peak memory estimates., NLSQStrategy enum should have the expected member values., Edge case: n_params=0 should not crash and should select STANDARD., TestNLSQStrategySelection (+61 more)

### Community 14 - "JAX JIT / vmap Primitives"
Cohesion: 0.03
Nodes (74): _fit_mcmc_jax_impl(), Internal implementation of fit_mcmc_jax., compute_data_statistics(), create_xdata_dict(), estimate_noise_scale(), extract_phi_info(), prepare_mcmc_data(), Data preparation and validation for CMC analysis.  This module provides utilitie (+66 more)

### Community 15 - "NLSQ Multi-Start & Bounds"
Cohesion: 0.03
Nodes (64): CMAESResult, CMAESWrapper, CMAESWrapperConfig, Configuration for CMA-ES wrapper.      Attributes     ----------     preset : st, Result from CMA-ES optimization.      Attributes     ----------     parameters :, Wrapper around NLSQ's CMAESOptimizer for homodyne integration.      This wrapper, Initialize CMA-ES wrapper.          Parameters         ----------         config, NLSQConfig (+56 more)

### Community 16 - "Test Mock Fixtures"
Cohesion: 0.03
Nodes (63): Higher param count results in fewer, larger shards., Higher param count results in fewer, larger shards., Integration tests for reparameterization in CMC., TestReparameterizationIntegration, ParameterSpace, Parameter space definition with bounds and prior distributions.      This class, Return a shallow copy safe for localized mutations., Return a copy with specific parameters removed. (+55 more)

### Community 17 - "NLSQ Config & CMA-ES"
Cohesion: 0.04
Nodes (73): _cache_validation_result(), _check_validation_cache(), clear_validation_cache(), _compute_data_hash(), _compute_data_statistics(), _compute_quality_score(), _generate_cache_key(), get_cache_stats() (+65 more)

### Community 18 - "CMC Data Prep & Sharding"
Cohesion: 0.03
Nodes (52): NLSQConvergenceError, Raised when NLSQ optimization fails to converge.      This exception indicates t, Error recovery strategies for NLSQ optimization failures.  This module defines e, Apply the specified recovery strategy.          Parameters         ----------, Add random perturbation to parameters.          Parameters         ----------, Check if another retry attempt should be made.          Parameters         -----, Apply recovery strategies for optimization failures.      This class implements, Initialize recovery strategy applicator.          Parameters         ---------- (+44 more)

### Community 19 - "Config Manager & YAML"
Cohesion: 0.03
Nodes (53): test_gamma_dot_recovery(), _compute_weights_jax(), create_shear_weighting(), Shear-Sensitivity Weighting for Anti-Degeneracy Defense.  This module implements, Configuration for shear-sensitivity weighting.      Attributes     ----------, Shear-sensitivity weighted loss for anti-degeneracy defense.      This class man, Compute angle weights for given phi0.          Performance Optimization (Spec 00, Update phi0 estimate from current parameters.          Parameters         ------ (+45 more)

### Community 20 - ".Fit() / Adapter.Py"
Cohesion: 0.03
Nodes (53): ConfigManager, Get the current configuration dictionary.          Returns         -------, Update a configuration value using dot notation.          Parameters         ---, Get angle filtering ranges., Minimal configuration manager for homodyne v2 scattering analysis.      Provides, Validate per-angle scaling array lengths against number of phi angles., Get CMC (Consensus Monte Carlo) configuration with validation and defaults., Get default CMC configuration.          T052: Logs default value application at (+45 more)

### Community 21 - "Weighter() / .  Init  ()"
Cohesion: 0.04
Nodes (50): _apply_auto_repair(), create_quality_controller(), DataQualityController, from_config_dict(), generate_quality_report(), QualityControlResult, QualityMetrics, Data Quality Controller for Homodyne =======================================  Co (+42 more)

### Community 22 - ".Copy() / .  Str  ()"
Cohesion: 0.04
Nodes (57): T037: End-to-end test of homodyne to NLSQ integration., End-to-end test: homodyne config -> NLSQ fit -> result., End-to-end: synthetic data -> NLSQAdapter.fit() -> result., TestFullRoundtripHomodyneToNlsq, AdapterConfig, CachedModel, _extract_nlsq_settings(), get_adapter() (+49 more)

### Community 23 - "Test Streaming Optimizer.Py / Test Confi"
Cohesion: 0.04
Nodes (63): Picklable worker class for parallel multi-start optimization.      This class en, _SingleFitWorker, check_zero_volume_bounds(), detect_degeneracy(), generate_random_starts(), _get_dataset_size(), get_n_workers(), _get_phi_from_data() (+55 more)

### Community 24 - ".  Init  () / .Get Bounds()"
Cohesion: 0.04
Nodes (61): _bounds_to_arrays(), _check_convergence(), _extract_shear_transform_config(), fit_nlsq_cmaes(), fit_nlsq_jax(), fit_nlsq_multistart(), _get_analysis_mode(), _get_default_initial_params() (+53 more)

### Community 25 - "Jit() / Grad()"
Cohesion: 0.03
Nodes (76): balanced_test_data(), dict_to_data_object(), imbalanced_test_data(), mock_config(), mock_xpcs_data(), Integration Tests for NLSQ Workflows ====================================  Conso, Create balanced test data for integration tests., Create imbalanced test data (skewed angle distribution). (+68 more)

### Community 26 - "From Config() / From Defaults()"
Cohesion: 0.03
Nodes (45): Comprehensive tests for NLSQ StreamingOptimizer integration.  Tests the integrat, Test configurable batch size., Test handling of partial last batch., Test that batch indices correctly map to data., Test that batches don't share data references., Test memory constancy during streaming optimization., Test that memory usage doesn't grow with number of batches., Test that batch data is released after processing. (+37 more)

### Community 27 - ".Run() / Main()"
Cohesion: 0.03
Nodes (51): build_parameter_labels(), classify_parameter_status(), convert_bounds_to_nlsq_format(), ExpandedParameters, Data Preparation Utilities for NLSQ Optimization.  This module provides data pre, Validate parameter bounds.      Args:         bounds: Bounds tuple (lower, upper, Validate and clip initial parameters to bounds.      Args:         params: Initi, Convert bounds to NLSQ-compatible format.      NLSQ expects bounds as (lower_arr (+43 more)

### Community 28 - "User Guide Index / Xpcsdataloader Class"
Cohesion: 0.03
Nodes (47): default_config(), mock_parameter_space(), _mock_scaling(), MockParameterSpace, MockPriorSpec, Tests for CMC NUTS sampler module.  Comprehensive tests for: - SamplingStats: Ti, Integration tests for sampling functionality., Test that config parameters are used correctly. (+39 more)

### Community 29 - "Valid Data() / Mock Loader()"
Cohesion: 0.04
Nodes (57): _compute_lpt_schedule(), _compute_threads_per_worker(), _generate_shard_keys(), _get_physical_cores(), _load_shared_array(), _load_shared_bytes(), _load_shared_dict(), _load_shared_shard_data() (+49 more)

### Community 30 - "Jit() / Vmap()"
Cohesion: 0.04
Nodes (43): _compute_beta_concentrations(), from_config(), from_defaults(), PriorDistribution, Parameter Space Configuration for MCMC/CMC =====================================, Validate distribution parameters., Convert to NumPyro distribution kwargs.          Returns         -------, Derive Beta concentration parameters on a scaled interval.      Parameters     - (+35 more)

### Community 31 - ".  Init  () / Testcaching"
Cohesion: 0.04
Nodes (63): _generate_cmc_diagnostic_plots(), Run the specified optimization method., Generate CMC/MCMC diagnostic plots using ArviZ.      This function generates 6 s, _run_optimization(), _apply_cli_overrides(), Apply CLI argument overrides to configuration.      Implements precedence: CLI a, _pool_mcmc_data(), _prepare_cmc_config() (+55 more)

### Community 32 - "Dict / .Fit()"
Cohesion: 0.03
Nodes (39): Integration Tests for Error Recovery =======================================  Er, Verify exception inheritance chain., NLSQConvergenceError must be a subclass of NLSQOptimizationError., NLSQNumericalError must be a subclass of NLSQOptimizationError., NLSQCheckpointError must be a subclass of NLSQOptimizationError., All custom exceptions must be subclasses of Exception., Catching NLSQOptimizationError must catch all subtypes., Verify error context is maintained through the exception chain. (+31 more)

### Community 33 - "Json Safe() / Testjsonsafe"
Cohesion: 0.05
Nodes (63): Bayesian Inference (CMC) Advanced Guide, CMA-ES for Multi-Scale Problems, Convergence Diagnostics Guide, Advanced Topics Section Index, Laminar Flow Advanced Guide, Per-Angle Modes Advanced Guide, Streaming Mode for Large Datasets, Laminar Flow Analysis Mode (7 parameters) (+55 more)

### Community 34 - "Testanglevalidation / Testoptimizationed"
Cohesion: 0.04
Nodes (47): Test 'auto' mode activation criteria., Test stratification decision with memory-based strategy selection., Test stratification with balanced angle distribution., Test stratification detects extreme angle imbalance., Test full integration: strategy selection + stratification decision., Test workflow when stratification is not needed (small dataset)., test_integration_stratification_with_strategy_selector(), test_integration_workflow_without_stratification() (+39 more)

### Community 35 - "Get Docs Path() / Testanalysismodes"
Cohesion: 0.03
Nodes (33): Comprehensive edge case tests for homodyne/data module.  This module tests edge, Test edge cases for flat config to nested config normalization., Flat config structure should be normalized to nested structure., Already nested config should not be modified., Test edge cases for correlation matrix reconstruction and correction., Reconstructed matrix should be symmetric., Diagonal values should be preserved after reconstruction., Single element matrix should work. (+25 more)

### Community 36 - "Get Docs Path() / Testcodeexamples"
Cohesion: 0.06
Nodes (40): create_quadratic_fit_function(), multistart_config(), Integration tests for multi-start NLSQ optimization.  Tests cover: - Full multi-, Integration tests for the complete multi-start workflow., Test that multi-start finds the global minimum., Test that results are reproducible with the same seed., Test that different seeds give different starting points., Test that the workflow handles failed optimization attempts. (+32 more)

### Community 37 - "Bounddict / Testbounddicttype"
Cohesion: 0.04
Nodes (29): Test validation catches invalid sample count., Tests for CMCConfig dataclass., Test validation catches invalid target accept probability., Test auto mode with small dataset returns False., Test auto mode with large dataset returns True., Test explicit True enables CMC regardless of data size., Test explicit False disables CMC regardless of data size., Test default configuration values. (+21 more)

### Community 38 - "Mockchunk / .  Call  ()"
Cohesion: 0.05
Nodes (36): _json_serializer(), JSON serializer for numpy arrays and other objects.      Delegates to homodyne.i, json_safe(), json_serializer(), JSON utility functions for homodyne I/O operations.  This module provides helper, Convert non-finite floats to JSON-safe representations.      JSON spec does not, Recursively convert numpy arrays and special types to JSON-safe types.      Para, JSON serializer for numpy arrays and other objects.      Use as the `default` ar (+28 more)

### Community 39 - "Log Calls() / Log Phase()"
Cohesion: 0.05
Nodes (35): Validate parsed command-line arguments.      Parameters     ----------     args, validate_args(), Test configuration file path validation., Test that missing config file is properly rejected., Test that existing config file is accepted., Test argument validation with valid and invalid methods., Test that validate_args accepts nlsq method., Test that validate_args accepts mcmc method. (+27 more)

### Community 40 - "Testcoordinateaxes / Test Data Loader.Py"
Cohesion: 0.06
Nodes (37): Configuration for internal reparameterization.      Attributes     ----------, Configuration for internal reparameterization.      Attributes     ----------, Transform physics params → sampling params.      Parameters     ----------     p, Transform physics params → sampling params.      Parameters     ----------     p, Transform sampling params → physics params (vectorized).      Parameters     ---, Transform sampling params → physics params (vectorized).      Parameters     ---, ReparamConfig, transform_to_physics_space() (+29 more)

### Community 41 - "Testnlsqfallback / Test Nlsq Core.Py"
Cohesion: 0.05
Nodes (32): get_docs_path(), Tests for research/theory documentation content.  Task 5.1: Focused tests for re, Test that shear rate equations are documented., Test citation format and BibTeX entries., Test that He et al. PNAS 2024 citation is present., Test research documentation structure and content., Test that BibTeX entry is present and valid., Test that DOI is properly formatted as a link. (+24 more)

### Community 42 - "Io.Py / Test Io.Py"
Cohesion: 0.05
Nodes (31): get_docs_path(), Tests for user guide documentation content., Test that quickstart.rst exists., Test that quickstart.rst includes YAML configuration example., Test that cli.rst exists., Test that cli.rst has required content., Test that configuration/index.rst exists., Test that user_guide/index.rst exists. (+23 more)

### Community 43 - "Jit() / Grad()"
Cohesion: 0.05
Nodes (32): JAX JIT-compatible stratified residual function for NLSQ optimization.  This mod, Extract q, L, dt from chunks (should be same for all chunks)., Extract unique phi, t1, t2 values from ALL chunks.          CRITICAL: Must extra, Create padded arrays with uniform size across all chunks.          Returns:, Compute residuals for a single padded chunk.          This function is designed, # NOTE: Warning for dt=None is emitted in __call__ (outside JIT trace), JIT-compatible stratified residual function using padded vmap.      This class s, # NOTE: Diagonal correction is intentionally skipped here. (+24 more)

### Community 44 - ".Test Str() / .Test Repr()"
Cohesion: 0.05
Nodes (42): adjust_covariance_for_transforms(), apply_forward_shear_transforms_to_bounds(), apply_forward_shear_transforms_to_vector(), apply_inverse_shear_transforms_to_vector(), build_per_parameter_x_scale(), build_physical_index_map(), format_x_scale_for_log(), normalize_param_key() (+34 more)

### Community 45 - "Combinedmodel / Model Static()"
Cohesion: 0.04
Nodes (28): Unit Tests for XPCS Data Loader ===============================  Tests for homod, Test JSON configuration file loading., Test configuration loading error handling., Test XPCS data loading functionality., Test loading data from mock HDF5 file., Test data loading with NPZ caching., Test data validation during loading., Property-based tests for XPCS loader. (+20 more)

### Community 46 - ". Make Config With Cmc() / Num Warmup=0 "
Cohesion: 0.05
Nodes (31): _chi_squared_jax(), _compute_c2_model_jax(), Unit Tests for JAX Backend Core Computations ===================================, Local helper: compute chi-squared goodness of fit., Expanded vectorization tests per TEST_REGENERATION_PLAN.md.      Tests broadcast, Test vectorization over phi angles., Test vectorization over different time array sizes., Test broadcasting with per-angle contrast/offset. (+23 more)

### Community 47 - "Gradientresult / Numpy Hessian()"
Cohesion: 0.05
Nodes (34): _adjust_covariance_for_normalization(), _compute_normalization_factors(), _denormalize_params(), fit_with_cmaes(), _format_bounds_summary(), _is_cmaes_available(), _normalize_bounds(), _normalize_params() (+26 more)

### Community 48 - "Async Io.Py / Asyncwriter"
Cohesion: 0.05
Nodes (26): AdvancedMemoryManager, Context manager entry., Context manager exit., Stop memory pressure monitoring., Advanced memory manager with intelligent allocation strategies.      Provides dy, Handle memory pressure warning.          Includes GC rate-limiting to avoid wast, Handle critical memory pressure., Handle memory pressure recovery. (+18 more)

### Community 49 - "Nlsqresult / .  Init  ()"
Cohesion: 0.06
Nodes (27): ParameterManager, Load parameter bounds from configuration and merge with defaults., Centralized parameter management system.      Handles:     - Parameter bounds (w, Initialize ParameterManager., Test default bounds for phi0 parameter., Test that bounds have required keys., Tests for parameter bounds management., Test default bounds for contrast parameter. (+19 more)

### Community 50 - ".Test Boundary Tolerance() / .Test Multi"
Cohesion: 0.04
Nodes (32): Unit Tests for NLSQ Core Functionality =======================================, Test NLSQ optimization functionality., Test NLSQ package availability detection., Test NLSQ fallback behavior when NLSQ package is not available., Test that module imports work without NLSQ package., Performance tests for NLSQ optimization., Test parameter helper functions (Phase 4.1)., Test validation integration in NLSQ (Phase 4.1). (+24 more)

### Community 51 - "Anglesubset / Simple Dataset()"
Cohesion: 0.06
Nodes (44): batch_chi_squared(), compute_chi_squared(), compute_g1_diffusion(), compute_g1_total(), compute_g2_scaled(), _compute_g2_scaled_core(), compute_g2_scaled_with_factors(), _create_gradient_fallback() (+36 more)

### Community 52 - "Testconfiggeneratorparser / .Test Parser"
Cohesion: 0.06
Nodes (28): Verify model caching works in integration context., clear_model_cache(), get_or_create_model(), Get cached model or create new one.      This function provides model instance c, Clear all cached models.      Returns:         Number of models removed from cac, model_func(), Model function for LeastSquares., clear_cache_before_each_test() (+20 more)

### Community 53 - "Protocol / .Compute G2()"
Cohesion: 0.05
Nodes (29): _estimate_contrast_offset_from_data(), NLSQResult, Result container for NLSQ optimization compatible with FitResult., Estimate contrast and offset from experimental g2 data.      For XPCS correlatio, Comprehensive edge case tests for homodyne/optimization module.  This module tes, Test edge cases for NLSQ parameter bounds., Bounds should be converted to arrays correctly for static mode., Bounds should be converted to arrays correctly for laminar mode. (+21 more)

### Community 54 - "Config.Py / Get Logger()"
Cohesion: 0.04
Nodes (32): config_invalid_prior(), config_missing_bounds(), config_partial_bounds(), laminar_flow_config_valid(), Unit Tests for Parameter Configuration =======================================, Configuration with missing parameter_space.bounds section., Configuration with only partial bounds (some parameters missing)., Configuration with invalid prior distribution parameters. (+24 more)

### Community 55 - "Model Func() / Testjitcompilation"
Cohesion: 0.05
Nodes (30): ConstraintSeverity, Parameter Manager for Homodyne ==================================  Centralized p, Severity levels for physics constraint violations., BoundDict, Parameter bound specification.      Attributes     ----------     name : str, Unit Tests for Parameter Manager Core ======================================  **, Test cross-parameter physics constraints., Test INFO when D_offset is large compared to D0. (+22 more)

### Community 56 - "Testparamcountbymode / Testgetmodelparam"
Cohesion: 0.07
Nodes (23): num_warmup=0 is rejected., Negative num_samples is rejected., Float num_chains is rejected (must be int)., Negative ESS threshold is rejected., R-hat threshold < 1.0 is rejected., Valid CMC configuration passes without errors., Invalid string computational backend is rejected., jax' as computational backend string is valid. (+15 more)

### Community 57 - "Model() / Models.Py"
Cohesion: 0.08
Nodes (41): _adaptive_gradient(), _backward_difference_single(), _central_difference_single(), _chunked_gradient_computation(), _complex_step_derivative(), _complex_step_gradient(), _compute_hessian_finite_diff(), DifferentiationConfig (+33 more)

### Community 58 - ".Run() / Pbs.Py"
Cohesion: 0.07
Nodes (36): _compute_mcmc_safe_d0(), create_init_strategy(), _extract_adapt_states(), _extract_step_sizes(), from_config(), _log_array_stats(), _preflight_log_density(), NUTS sampler wrapper for CMC analysis.  This module provides utilities for runni (+28 more)

### Community 59 - "Reparamconfig / Testreparamconfig"
Cohesion: 0.06
Nodes (18): Tests for async I/O utilities., Test that wait_all returns errors rather than raising., Test thread-based data prefetching., Test that calling shutdown() twice is safe., Test that exceptions in load_fn are re-raised on __next__., Test background result writing., TestAsyncWriter, TestPrefetchLoader (+10 more)

### Community 60 - ".  New  () / Get Bounds()"
Cohesion: 0.06
Nodes (41): AngleSubset, combine_angle_results(), Data subset for a single phi angle.      Attributes     ----------     phi_angle, Split dataset into per-angle subsets.      Parameters     ----------     phi : n, Combine per-angle optimization results.      Parameters     ----------     per_a, split_data_by_angle(), imbalanced_dataset(), Unit Tests for Sequential Per-Angle Optimization  Tests the sequential_angle.py (+33 more)

### Community 61 - "Types.Py / Cmcconfig"
Cohesion: 0.05
Nodes (22): Test that -i short option works for interactive., Test that -v short option works for validate., Test that -f short option works for force., Test combining mode and output arguments., Test combining mode and force arguments., Test parser with no arguments (all defaults)., Tests for homodyne-config argument parser., Test that create_parser returns ArgumentParser. (+14 more)

### Community 62 - ".Fit() / .Check()"
Cohesion: 0.07
Nodes (26): _apply_angle_filtering_for_optimization(), Apply angle filtering to data before optimization.      This function filters ph, create_phi_filtering_config(), Create a phi_filtering configuration dictionary.      Parameters     ----------, Integration tests for MCMC optimization with angle filtering., Test that MCMC receives correctly filtered angle data., Test that dataset size reduction is measurable (9 → 3 angles)., Test that log messages confirm correct angle selection for MCMC. (+18 more)

### Community 63 - "Save Nlsq Results() / Testcomputenlsqfit"
Cohesion: 0.07
Nodes (38): apply_config_defaults(), ConfigValidationResult, create_example_yaml_config(), load_json_config(), load_yaml_config(), migrate_json_to_yaml_config(), Configuration System for XPCS Data Loading =====================================, Load YAML configuration file.      Args:         config_path: Path to YAML confi (+30 more)

### Community 64 - "Jit() /   Init  ()"
Cohesion: 0.06
Nodes (25): get_model_param_count(), Get total number of sampled parameters.      Parameters     ----------     n_phi, Get total number of sampled parameters.      Parameters     ----------     n_phi, Tests for get_model_param_count function., Static mode with auto per-angle has 6 params., Laminar flow with auto per-angle has 10 params., Laminar flow with individual per-angle scales with n_phi., Constant mode has no sampled scaling params. (+17 more)

### Community 65 - ".Run() / Pjit.Py"
Cohesion: 0.06
Nodes (22): PBSBackend, PBS (Portable Batch System) backend for CMC HPC cluster execution.  This module, PBS backend for HPC cluster MCMC execution.      Submits each data shard as a se, Initialize PBS backend., Check if PBS commands are available., Get backend name.          Returns         -------         str             Backe, Check if PBS backend is available.          Returns         -------         bool, Run MCMC sampling via PBS job submission.          Parameters         ---------- (+14 more)

### Community 66 - "Is Linux() / Is Macos()"
Cohesion: 0.05
Nodes (39): mock_stratified_data_small(), physical_param_names_laminar(), physical_param_names_static(), Unit tests for StratifiedResidualFunction.  Tests the angle-stratified residual, Physical parameter names for static_mode mode., Physical parameter names for laminar_flow mode., Test StratifiedResidualFunction initialization with per-angle scaling., Test initialization with laminar_flow parameters. (+31 more)

### Community 67 - "Full Params() / Shear Params()"
Cohesion: 0.06
Nodes (27): _compute_g1_diffusion_core(), Compute diffusion contribution to g1 using reference implementation approach., compute_g1_diffusion(), _compute_g1_diffusion_elementwise(), Element-wise diffusion computation for CMC shards using trapezoidal cumulative s, Compute g1 diffusion for CMC element-wise paired arrays.      CMC-specific funct, # TODO: This file tests low-level function consistency, not integration., Verify NLSQ and CMC physics functions produce identical output.          This is (+19 more)

### Community 68 - "Main() / .Log()"
Cohesion: 0.09
Nodes (26): Save complete NLSQ optimization results to structured directory.      Main orche, save_nlsq_results(), create_mock_config_manager(), create_mock_data_dict(), create_mock_optimization_result(), Factory for creating mock OptimizationResult objects for testing.  This module p, Create mock ConfigManager dict for testing metadata extraction.      Parameters, Create mock experimental data dictionary for testing.      Parameters     ------ (+18 more)

### Community 69 - ".  Init  () / .End Phase()"
Cohesion: 0.06
Nodes (22): Select appropriate backend based on configuration.      Parameters     ---------, select_backend(), MultiprocessingBackend, CMC backend using Python multiprocessing.      Runs MCMC sampling in parallel ac, Check if multiprocessing is available., PjitBackend, JAX pjit backend for CMC distributed execution.  This module provides distribute, JAX pjit backend for distributed MCMC execution.      Uses JAX's pjit for parall (+14 more)

### Community 70 - "Synthetic C2 Data() / Testnlsqperformanc"
Cohesion: 0.06
Nodes (21): T010: Tests for AnalysisSummaryLogger class., Summary logger initializes with run_id and mode., Phases are tracked with timing., Metrics are recorded correctly., Output files are tracked., Convergence status is set., Warning and error counts are tracked., log_summary() outputs structured summary. (+13 more)

### Community 71 - "Testmalformedconfigfiles / Test Config V"
Cohesion: 0.05
Nodes (37): benchmark_config(), cleanup_jax_state(), is_linux(), is_macos(), is_windows(), jax_backend(), mock_hdf5_file(), mock_mcmc_samples() (+29 more)

### Community 72 - "Sequential.Py /  Jax Jacobian()"
Cohesion: 0.05
Nodes (25): API Compatibility Tests =======================  Tests for API stability and bac, Test function signature compatibility., Test core function signatures are stable., Test optimization function signatures are stable., Test data loader function signatures are stable., Test return type compatibility., Test data loader return types are consistent., Test error handling consistency. (+17 more)

### Community 73 - "Parser() / Mock Config()"
Cohesion: 0.07
Nodes (25): detect_total_system_memory(), get_adaptive_memory_threshold(), Memory Management and Unified Strategy Selection for NLSQ Optimization.  Provide, Detect total system memory in bytes using multiple methods.      Returns     ---, Compute adaptive memory threshold based on system memory.      The memory thresh, Estimate peak memory usage for stratified least-squares optimization., Determine if streaming optimizer should be used based on memory estimate., estimate_memory_for_stratified_ls() (+17 more)

### Community 74 - ".With Info() / Resultbuilder"
Cohesion: 0.08
Nodes (21): main(), Run all system tests (9 tests total)., Run quick critical tests only (for fast CI/CD feedback)., Calculate overall system health score (0-100) across 9 validation tests., Test homodyne package installation., Generate comprehensive validation report., Main function for system validation CLI., Test shell completion system. (+13 more)

### Community 75 - ".  Call  () / .  Init  ()"
Cohesion: 0.07
Nodes (35): _coerce_mapping_to_array(), _coerce_numeric_array(), _compute_final_jacobian_norms(), _estimate_initial_jacobian_norms(), _get_nlsq_engine(), _jax_jacobian(), _normalize_least_squares_kwargs(), optimize_per_angle_sequential() (+27 more)

### Community 76 - "Test Get Diagnostics() / Test Stratified"
Cohesion: 0.07
Nodes (20): Builder for constructing OptimizationResult objects.      Provides a fluent inte, 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. (+12 more)

### Community 77 - "Testapplyanglefiltering /  Apply Angle F"
Cohesion: 0.08
Nodes (17): get_device_info(), Get comprehensive device and backend information., GradientCapabilityMixin, _PhysicsModelProtocol, Check if gradient computation is available., Get the best available gradient method for optimization algorithms., Get comprehensive gradient capability information., Generate human-readable backend summary. (+9 more)

### Community 78 - "Testnlsqwrapperfit / .Test Fit Logs Iter"
Cohesion: 0.08
Nodes (34): CMCBackendConfig, CMCCombinationConfig, CMCConfig, CMCInitializationConfig, CMCPerShardMCMCConfig, CMCShardingConfig, CMCValidationConfig, ExperimentalDataConfig (+26 more)

### Community 79 - "Safe Len() / Testsafelen"
Cohesion: 0.08
Nodes (24): Convert parameter array to named dictionary., JAX-safe length function that handles scalars, arrays, and JAX objects.      Arg, safe_len(), Unit Tests for homodyne.core.physics_utils Module ==============================, Test safe_len with numpy scalar (0-d array)., Test safe_len with Python list., Test safe_len with Python tuple., Test safe_len with empty list. (+16 more)

### Community 80 - "Tmp Hdf5 Dir() / Synthetic Hdf5()"
Cohesion: 0.08
Nodes (19): BenchmarkingMixin, OptimizationRecommendationMixin, Mixins for physics model capabilities.  This module provides reusable mixin clas, Mixin providing performance benchmarking capabilities.      This mixin adds meth, Mixin providing optimization guidance.      This mixin adds methods for getting, DiffusionModel, PhysicsModelBase, Physical Models for Homodyne ================================  Object-oriented i (+11 more)

### Community 81 - "Test Config Error Paths.Py / Testconfigv"
Cohesion: 0.07
Nodes (20): Validate parameter values against bounds with detailed error reporting.      Thi, validate_parameters_detailed(), Test that validation passes with valid initial parameters., Test that validation catches out of bounds parameters., Test that validation error messages include parameter names., Unit Tests for homodyne.core.physics Module ====================================, Test validation with multiple parameters out of bounds., Test validation without parameter names. (+12 more)

### Community 82 - "Data Prep.Py / Validate Bounds()"
Cohesion: 0.07
Nodes (23): BenchmarkingMixin, CombinedModel, Validate parameter values against bounds and constraints., Combined diffusion + shear model for complete homodyne analysis.      This is th, Compute g1 for a batch of points using vmap.          Performance Optimization (, Get bounds appropriate for analysis mode., Get default parameters appropriate for analysis mode., GradientCapabilityMixin (+15 more)

### Community 83 - "Valueerror / .To Fourier()"
Cohesion: 0.08
Nodes (21): get_param_names_in_order(), Get parameter names in NumPyro sampling order.      CRITICAL: This order must ma, constant_averaged mode should not include contrast/offset params., constant and constant_averaged should produce same param names., Bug P1: fixed_contrast/offset must be passed for constant_averaged mode., TestStage4ConstantAveragedScaling, Tests for parameter name ordering with different modes., Test parameter names for individual mode static analysis. (+13 more)

### Community 84 - "Mockchunk / Mockchunkeddata"
Cohesion: 0.06
Nodes (20): Unit Tests for Configuration Validation ========================================, Test handling of invalid parameter values., Test with NaN values in initial parameters., Test with infinity values., Test that negative D0 values should be caught during validation., Test type mismatch: string instead of float., Test with very large parameter values., Test with very small but positive parameter values. (+12 more)

### Community 85 - ".Test Symmetry() / .Test Non Negative()"
Cohesion: 0.06
Nodes (18): Tests for NLSQWrapper.fit() method (15 tests)., TC-FIT-001: fit() returns OptimizationResult object., TC-FIT-002: fit() accepts v2.4.0 per-angle parameter structure., TC-FIT-003: fit() validates parameter bounds., TC-FIT-004: fit() handles successful convergence., TC-FIT-005: fit() handles max iterations without convergence., TC-NLSQ-010: Bounds violation triggers 10% perturbation retry., TC-FIT-006: fit() detects NaN and resets. (+10 more)

### Community 86 - ".Cleanup() / .  Init  ()"
Cohesion: 0.09
Nodes (34): Anti-Degeneracy Defense System, Bimodal Posterior Detection, CheckpointManager Fault Tolerance, CMC Data Preparation (prepare_mcmc_data), CMC Fitting Architecture, CMC Five Model Variants, ConfigManager System, Consensus Monte Carlo Combination (+26 more)

### Community 87 - "Testnlsqconfigvalidation / .Test Invalid"
Cohesion: 0.08
Nodes (22): Integration tests for the enhanced logging system.  Tests for: - T014: Logging i, T014a: Tests for logging fallback when file write fails., System continues with console logging when file write fails., Logging continues when file logging is disabled., Tests for external library log suppression (T011)., JAX logger is set to WARNING by default., NumPy logger is set to WARNING by default., User module overrides can override default suppression. (+14 more)

### Community 88 - "Jit() / Grad()"
Cohesion: 0.06
Nodes (21): _create_synthetic_hdf5_aps_old(), Integration Tests for HDF5 Pipeline ======================================  End-, Verify the HDF5 -> XPCSDataLoader path for static mode., XPCSDataLoader should auto-detect APS old format., Loaded data dict must contain all keys consumed by NLSQ., Array dimensions must be internally consistent., Per loader contract, 1-D time arrays start at t=0., No NaN or Inf should appear in loaded correlation data. (+13 more)

### Community 89 - ".Close() / .Close()"
Cohesion: 0.08
Nodes (27): DatashaderRenderer, plot_c2_comparison_fast(), plot_c2_heatmap_fast(), Datashader backend for fast C2 heatmap visualization (CPU-only in v2.3.0+).  Thi, Get Datashader-compatible colormap.          Datashader accepts:         1. List, Plot C2 heatmap using Datashader for fast CPU rendering.      This function uses, Fast heatmap rendering using Datashader (CPU-only in v2.3.0+).      This rendere, Generate 3-panel comparison plot using Datashader CPU rendering.      Replaces g (+19 more)

### Community 90 - ".To Dict() / From Dict()"
Cohesion: 0.07
Nodes (18): Tests for configuration validation error paths.  Tests ConfigManager._validate_c, Test validate_per_angle_scaling() error handling., Helper to create ConfigManager with per-angle scaling., Contrast array with wrong length raises ValueError., Offset array with wrong length raises ValueError., Single-element contrast array warns when n_phi > 1., Single-element offset array warns when n_phi > 1., Matching array lengths produce no errors or warnings. (+10 more)

### Community 91 - "Testvalidatesavepath / Validate Save Pat"
Cohesion: 0.08
Nodes (22): Compute and store fixed per-angle contrast/offset from quantiles.          This, compute_quantile_per_angle_scaling(), Estimate per-angle contrast/offset from quantiles of c2_experimental values., MockChunk, MockChunkedData, MockStratifiedData, Tests for quantile-based per-angle contrast/offset estimation.  This module test, Test that uniform contrast/offset is recovered accurately. (+14 more)

### Community 92 - " Plot Ess() /  Plot Rhat()"
Cohesion: 0.11
Nodes (31): configure_xla_mode(), detect_shell_type(), get_venv_path(), get_xla_config_source_path(), install_completion_activation(), _install_completion_bash_activation(), _install_completion_fish_activation(), install_xla_activation() (+23 more)

### Community 93 - "Testphysicsconstraints /  Compute C2 Mod"
Cohesion: 0.08
Nodes (27): apply_diagonal_correction(), Apply diagonal correction to a single correlation matrix.      This function rep, correlation_matrix_1001x1001(), identity_diagonal_matrix(), Comprehensive Test Suite for Diagonal Correction  Tests the unified diagonal_cor, Tests for different backends in unified module., Test explicit NumPy backend selection., Test auto backend detection with NumPy input. (+19 more)

### Community 94 - ".Test Zero D0() / .Test Positive Output("
Cohesion: 0.07
Nodes (25): _load_data(), normalize_angle_to_symmetric_range(), Command Dispatcher for Homodyne CLI ======================================  Hand, Placeholder when XPCSDataLoader is not available., Normalize angle(s) to [-180, 180] range.      This is a wrapper that delegates t, Load experimental data using XPCSDataLoader.      Uses XPCSDataLoader which prop, XPCSDataLoader, Unit Tests for CLI Core Functionality ======================================  ** (+17 more)

### Community 95 - "Safe Sinc() / Testsafesinc"
Cohesion: 0.06
Nodes (17): Test NLSQConfig.validate method., Test that valid config returns no errors., Test validation catches invalid loss function., Test all valid loss functions pass validation., Test validation catches non-positive trust_region_scale., Test validation catches non-positive tolerances., Test validation catches non-positive max_iterations., Test validation catches non-positive chunk sizes. (+9 more)

### Community 96 - "Testdtpropagation / Testtimegridgenerati"
Cohesion: 0.07
Nodes (22): categorize(), DatasetSize, estimate_scaling_parameters(), FitResult, Unified Homodyne Model with JAX-Accelerated Least Squares ======================, Dataset size categories for optimization., Results from unified homodyne model fitting.      Contains both physical and sca, Get comprehensive fit summary. (+14 more)

### Community 97 - "Tmp Output Dir() / Testcliinvalidconfig"
Cohesion: 0.1
Nodes (30): API Reference Index, Architecture Index, CMC Sampler / SamplingPlan API Doc, Adaptive Sampling (SamplingPlan reduces warmup/samples for small shards), ADR-5: Auto-mode averages per-angle scaling to 2 params (prevents parameter absorption degeneracy), Data Flow: YAML→ConfigManager→XPCSDataLoader→HomodyneModel→NLSQ/CMC→Result, Laminar Flow Analysis Mode (7 params), NUMA-aware CPU topology for CMC worker pinning (+22 more)

### Community 98 - "Theory.Py / .  Init  ()"
Cohesion: 0.09
Nodes (17): Test that extension check is case-insensitive., Test parent directory must exist when required., Test parent directory not checked when not required., Test that parent path must be a directory., Test that resolved path stays within base_dir., Test that Path objects are accepted., Test validate_save_path function., Test that None input returns None. (+9 more)

### Community 99 - ".Fit() / Is Available()"
Cohesion: 0.09
Nodes (27): _create_empty_figure(), plot_arviz_pair(), plot_arviz_posterior(), plot_arviz_trace(), ArviZ-Based MCMC Plotting Functions.  Provides ArviZ-powered trace, posterior, a, Plot posterior distributions with 95% credible intervals using ArviZ.      Param, Create an empty figure with a message., Plot pair plots showing parameter correlations using ArviZ.      Parameters (+19 more)

### Community 100 - "Compute G1() / Compute G1 Shear()"
Cohesion: 0.09
Nodes (19): calculate_diffusion_coefficient(), Calculate time-dependent diffusion coefficient using discrete evaluation.      F, Integration tests for error handling across modules., Test handling of edge cases in time arrays., Test handling of extreme physics parameters., Integration tests for configuration handling., Test workflow starting from YAML configuration., Test workflow starting from JSON configuration. (+11 more)

### Community 101 - "Main() / Set Mode()"
Cohesion: 0.07
Nodes (19): Unit Tests for Simulated Data Plotting Fixes ===================================, Test that time grid is deterministic given only config parameters., Test that dt parameter is correctly propagated through the call chain., Test difference between explicit dt and estimated dt., Test time grid generation for simulated data plotting., Tests to prevent regression of the identified bugs., Ensure simulated data time grid doesn't depend on exp data., Test that time_max uses correct formula with (n-1). (+11 more)

### Community 102 - "Logging.Py / .Process()"
Cohesion: 0.07
Nodes (19): Integration Tests for CLI Pipeline =====================================  CLI in, Test homodyne-config generation in laminar_flow mode., homodyne-config -m laminar_flow should create a valid YAML file., Generated laminar_flow config must be parseable YAML., Laminar flow config should include shear-related parameter names., Test CLI error handling for invalid invocations., Running homodyne-config without --mode should exit non-zero., Generating to an existing path without --force should fail. (+11 more)

### Community 103 - "Get Venv Path() / Post Install.Py"
Cohesion: 0.09
Nodes (17): HDF5FileFactory, Generate theoretical correlation function.          WARNING: SIMPLIFIED PHYSICS, Add realistic experimental artifacts., Create dataset with multiple q-values.          Parameters         ----------, Create time-series XPCS dataset.          Parameters         ----------, Create dataset with specific noise characteristics.          Parameters, Create edge case datasets for testing robustness.          Parameters         --, Factory for creating mock HDF5 files. (+9 more)

### Community 104 - ".  Str  () / Test Physics.Py"
Cohesion: 0.1
Nodes (19): batch_computation(), compute_chi2_theory(), compute_chi_squared(), compute_g1(), compute_g2(), compute_g2_theory(), Theory Computation Engine for Homodyne =========================================, Estimate computational cost for given data dimensions.          Helps with perfo (+11 more)

### Community 105 - ".  Repr  () / .Is Parameter Active()"
Cohesion: 0.07
Nodes (17): compute_g1_shear(), Wrapper function that computes g1 shear using configuration dt.      IMPORTANT:, compute_g1(), Test core JAX computational functions., Test JAX availability matches module state., Test basic g1 diffusion computation., Test g1 diffusion symmetry properties., Test basic g1 shear computation. (+9 more)

### Community 106 - "Message() / .Tolist()"
Cohesion: 0.09
Nodes (21): Tests for XLA configuration CLI., Valid mode should write config file and return True., Invalid mode should return False without writing., Should write config to per-venv path when VIRTUAL_ENV is set., All modes in VALID_MODES should be accepted., Tests for detect_optimal_devices., Should always return a positive integer., Should return 2, 4, 6, or 8. (+13 more)

### Community 107 - "Path Validation.Py / Testsanitizelogpath"
Cohesion: 0.08
Nodes (14): Extract base parameter name from indexed parameter names.          Handles per-a, Get parameter bounds configuration (with caching for performance).          Para, Get list of active (physical) parameters from configuration (cached).          T, Get default active parameters based on analysis mode., Get all parameter names including scaling parameters.          Returns         -, Get the effective number of physical parameters (excludes scaling).          Ret, Get total number of parameters including scaling parameters.          Returns, Validate parameter values against bounds.          Parameters         ---------- (+6 more)

### Community 108 - "Testtoworkflowkwargsvalid / Random Sampl"
Cohesion: 0.09
Nodes (20): completion_script_path(), _extract_all_completion_flags(), _extract_argparse_flags(), _extract_completion_flags_for_command(), Completion parity tests.  Verifies that shell completion scripts are in sync wit, All homodyne-config CLI flags should appear in _homodyne_config()., Flags in _homodyne() should correspond to actual argparse flags., Flags in _homodyne_config() should correspond to actual argparse flags. (+12 more)

### Community 109 - "Testcompletionaliases / .Test Aliases Pr"
Cohesion: 0.09
Nodes (24): fit_mcmc_jax(), Run CMC (Consensus Monte Carlo) analysis on XPCS data.      This function signat, fit_mcmc_jax should infer dt from pooled time axes when none is provided., test_force_random_sharding_override(), test_stratified_allowed_for_single_angle(), Integration Tests for MCMC Workflows =====================================  **Up, Generate simple synthetic data for static mode testing.      Uses known paramete, Test MCMC accepts manual initial_params parameter.      Verifies that initial_pa (+16 more)

### Community 110 - "Testnaninfinjection / .Test Inf In Loss("
Cohesion: 0.07
Nodes (16): Unit tests for angle filtering functionality.  Tests the _apply_angle_filtering_, Test edge cases and error conditions., Test handling of empty phi angles array., Test filtering with negative angle values., Test filtering with angles > 360 degrees., Tests for angle normalization to [-180°, 180°] range., Test normalization of angles in (180°, 360°) range., Test normalization of angles in (-360°, -180°) range. (+8 more)

### Community 111 - "Testanglenormalization / Test Angle Filt"
Cohesion: 0.07
Nodes (15): Test NaN detection in loss value., Test Inf detection in loss value., Test negative Inf detection in loss value., Test detection of multiple NaN values., Test detection of mixed NaN/Inf values., Test that valid gradients don't raise exception., Test that valid parameters within bounds don't raise exception., Test that parameter bounds violations raise exception. (+7 more)

### Community 112 - "Mock Data() / Mock Result()"
Cohesion: 0.08
Nodes (15): Convert Fourier coefficients to per-angle contrast/offset.          Parameters, Convert a single per-angle array to Fourier coefficients.          Convenience m, Convert Fourier coefficients to per-angle values for a single group.          Co, Validate inputs and cache computed values., Transform multi-dimensional XPCS data to flattened 1D arrays.          Args:, Validate initial parameters are within bounds, clip if necessary.          Args:, Convert homodyne bounds format to NLSQ format.          Args:             homody, Create JAX-compatible model function for NLSQ with per-angle scaling support. (+7 more)

### Community 113 - "Compute T Ref() / Testcomputetref"
Cohesion: 0.09
Nodes (20): _build_formatter(), _ColorFormatter, _ContextAdapter, get_logger(), _get_memory_gb(), log_calls(), log_operation(), log_performance() (+12 more)

### Community 114 - ".  Exit  () / .Shutdown()"
Cohesion: 0.11
Nodes (25): BaselineResults, benchmark_full_fit(), benchmark_residual_evaluation(), benchmark_vectorization_opportunity(), compare_with_baseline(), create_benchmark_config(), create_benchmark_dataset(), from_dict() (+17 more)

### Community 115 - ".Test Import() / .Test No Data Loss()"
Cohesion: 0.11
Nodes (18): compute_g2_batch(), compute_g2_batch_with_per_angle_scaling(), compute_theoretical_fits(), Fit Computation Utilities for NLSQ Results.  This module provides functions for, Compute g2 with per-angle contrast/offset in single vectorized operation.      P, Batch least squares solving for all angles.      Performance Optimization (Spec, Compute theoretical fits with per-angle least squares scaling.      Generates th, Compute g2 for all phi angles in a single vectorized operation.      Performance (+10 more)

### Community 116 - "Recovery.Py / Diagnose Error()"
Cohesion: 0.1
Nodes (20): _configure_cpu_optimal(), configure_optimal_device(), get_device_status(), Device Optimization Module for Homodyne ========================================, Get current device status and capabilities.      Returns     -------     dict, # IMPORTANT: Don't set JAX_PLATFORMS - let JAX auto-detect available backend, Automatically configure the optimal CPU device for homodyne analysis.      Confi, Configure optimal CPU settings. (+12 more)

### Community 117 - " Array To Params() /  Params To Array()"
Cohesion: 0.1
Nodes (16): compute_t_ref(), Compute reference time as geometric mean of time range.      Parameters     ----, Compute reference time as geometric mean of time range.      Parameters     ----, compute_t_ref raises ValueError for non-positive inputs., Replicate core.py's try/except pattern with invalid inputs.          This tests, With valid inputs, fallback_value is ignored., NaN inputs with fallback return the fallback value., Tests for compute_t_ref function. (+8 more)

### Community 118 - "Test Nlsq Ooc Routing.Py / Testoutofcore"
Cohesion: 0.1
Nodes (15): Shard data with balanced angle coverage per shard.      This is the preferred sh, shard_data_angle_balanced(), Tests for shard_data_angle_balanced function (v2.19.0+).      This function ensu, Test shard_data_angle_balanced is importable., Test basic angle-balanced sharding creates valid shards., Test each shard has good angle coverage., Test data is distributed proportionally across shards., Test single-angle data falls back to random sharding. (+7 more)

### Community 119 - "Testoptimizationstrategy / .Test Strateg"
Cohesion: 0.08
Nodes (20): diagnose_error(), execute_with_recovery(), Error recovery and diagnostics for NLSQ optimization.  Extracted from wrapper.py, Extract uncertainties with diagonal regularization for singular pcov., Diagnose optimization error and provide actionable recovery strategy (T023)., Execute optimization with automatic error recovery (T022-T024).      Implements, safe_uncertainties_from_pcov(), Execute optimization with automatic error recovery (T022-T024). (+12 more)

### Community 120 - "Logconfiguration / Worker Function()"
Cohesion: 0.11
Nodes (17): _array_to_params(), _params_to_array(), Convert parameter dictionary to array., Convert parameter array to dictionary.      Returns JAX arrays as-is to avoid tr, Converting array to params should preserve values for static mode., Converting array to params should preserve values for laminar mode., Params -> array -> params roundtrip should preserve values for static., Params -> array -> params roundtrip should preserve values for laminar. (+9 more)

### Community 121 - "Jit() /  Is Jax Array()"
Cohesion: 0.08
Nodes (16): create_progress_callback(), create_streaming_progress_callback(), HomodyneIterationLogger, MultiStartProgressTracker, ProgressConfig, Progress bar and logging callbacks for NLSQ optimization.  This module provides, Log iteration information based on verbosity settings., Create progress callback chain for NLSQ optimization.      Creates a callback ch (+8 more)

### Community 122 - "Rng() / Simple Matrix()"
Cohesion: 0.08
Nodes (15): Unit Tests for Anti-Degeneracy Pre-Check and Out-of-Core Routing Fix (v2.22.0) =, T090e: Memory routing uses effective count, not expanded.          This is the c, T090f: static mode with 3 angles, auto → auto_averaged (5 params)., Tests for the multi-criteria convergence logic.      The old convergence used ||, T090g: Norm-based convergence is scale-sensitive (old behavior).          Demons, T090h: ftol prevents convergence when chi2 still improving., T090i: Convergence requires BOTH xtol AND ftol., T090j: rel_change must be initialized before loop to prevent NameError. (+7 more)

### Community 123 - ".Test Get Prior Means() / .Test Get Boun"
Cohesion: 0.08
Nodes (14): Tests for optimization strategy selection (12 tests)., TC-NLSQ-020: <1M points uses STANDARD strategy., TC-NLSQ-021: 1M-10M points uses LARGE strategy., TC-NLSQ-022: 10M-100M points uses CHUNKED strategy., TC-NLSQ-023: >100M points uses STREAMING strategy., TC-STRATEGY-001: Exact 1M boundary uses LARGE., TC-STRATEGY-002: Exact 10M boundary uses CHUNKED., TC-STRATEGY-003: Exact 100M boundary uses STREAMING. (+6 more)

### Community 124 - "Testbetascaledintegration / Static Confi"
Cohesion: 0.1
Nodes (17): get_xpcs_model(), Get the appropriate NumPyro model function for the given per-angle mode.      Pa, Get the appropriate NumPyro model function for the given per-angle mode.      Pa, Fix 5: Wire reparameterized model for auto + laminar_flow., auto + use_reparameterization should return reparameterized model., auto without reparameterization should return averaged model., constant_averaged should return constant_averaged model., Reparameterization flag should be ignored for constant_averaged. (+9 more)

### Community 125 - ".Test Diagnostics() / .Test Reset Monito"
Cohesion: 0.09
Nodes (15): _compute_g1_diffusion_jax(), Local helper: compute g1 diffusion factor., Expanded numerical stability tests per TEST_REGENERATION_PLAN.md.      Tests: Un, Test no underflow for large time separations (tau)., Test no overflow for very small time separations., Test precision handling in subtraction of similar values., Test stability with extreme q values., Test stability with extreme diffusion coefficients. (+7 more)

### Community 126 - " Apply Cli Overrides() / Test Overriding"
Cohesion: 0.1
Nodes (15): create_stratified_residual_function(), Residual function that respects angle-stratified chunk structure.      This clas, DEPRECATED: Dead code path -- not called from any live execution path., JAX-native residuals for use in JIT/Jacobian contexts.          Performance Opti, Vectorized residual computation using concatenated arrays.          Performance, Original chunk-based residual computation — REMOVED.          Per-chunk data was, Validate that all chunks contain all phi angles.          This is a critical val, Get diagnostic information about the residual function.          Returns: (+7 more)

### Community 127 - ".Test Valid Eps Path() / .Test Valid Pdf"
Cohesion: 0.09
Nodes (14): compute_fitted_c2(), create_inference_data(), from_mcmc_samples(), _get_scaling_base(), ParameterStats, CMC result dataclass and ArviZ integration.  This module provides the CMCResult, Return the base scaling name if *name* is an indexed scaling param, else None., Get posterior statistics for each parameter.          Returns         ------- (+6 more)

### Community 128 - "Testjaxgradientflow / Testjaxfancyindexi"
Cohesion: 0.08
Nodes (14): Unit tests for JAX operations and indexing behavior.  This test suite verifies t, Test fancy indexing with random out-of-order indices., Test boolean mask indexing (another form of fancy indexing).          Note: Bool, Test JAX gradient computation through indexed operations., Verify gradients flow correctly through fancy indexing operations., Test gradient when both array values and indexing depend on parameters., Test JAX fancy indexing with traced indices in JIT-compiled functions., Test fancy indexing with small array (1k elements) and traced indices. (+6 more)

### Community 129 - ".  Call  () /  Get Param Names()"
Cohesion: 0.1
Nodes (16): Regression tests for previously identified bugs., Test that XPCS data format (c2_exp) calculates dataset size correctly., Test that custom starting points are included in multi-start.          Regressio, Test that initial_params are loaded from config when not provided.          Regr, TestRegressionFixes, generate_lhs_starts(), include_custom_starts(), Generate starting points via Latin Hypercube Sampling.      Parameters     ----- (+8 more)

### Community 130 - "Test Sphinx Rst Formatting() / Test Conf"
Cohesion: 0.09
Nodes (15): _get_param_names(), Get parameter names for a given analysis mode.      Parameters     ----------, Run a single NLSQ fit.          Parameters         ----------         fit_data :, Test _get_param_names for static mode., Test _get_param_names for laminar flow mode., Test that analysis_mode matching is case insensitive., Test edge cases for parameter name retrieval., Static mode should have 5 parameter names. (+7 more)

### Community 131 - "Temp Dir() / Xpcs Config()"
Cohesion: 0.08
Nodes (16): Unit tests for the BetaScaled prior fallback pathway.  Exercises the stable-prio, Configuration with TruncatedNormal priors., Ensure ParameterSpace can emit BetaScaled priors., Test converting all TruncatedNormal priors to Beta., Test converting mixed prior types preserves unbounded., Test that conversion preserves mu and sigma for Beta computation., Test that conversion doesn't modify original ParameterSpace., Test converting empty ParameterSpace. (+8 more)

### Community 132 - "Datasetmetadata / .Create 1B Dataset()"
Cohesion: 0.08
Nodes (13): Tests for ParameterSpace instance methods., Test getting bounds for valid parameter., Test getting bounds for invalid parameter raises KeyError., Test getting prior for valid parameter., Test getting prior for invalid parameter raises KeyError., Test getting bounds as numpy arrays., Test getting prior means as numpy array., Test validating parameter values that are all within bounds. (+5 more)

### Community 133 - "Main() / .To Dict()"
Cohesion: 0.08
Nodes (23): Unit tests for developer guide and configuration documentation.  Tests validate, Test that configuration/options.rst exists., Test that developer/index.rst exists., Test that developer guide references CLAUDE.md for commands., Test that configuration templates reference the YAML templates., Test that internal links in developer guide are properly formatted., Test that internal links in configuration guide are properly formatted., Test that RST files have proper formatting. (+15 more)

### Community 134 - "Physics.Py / Parameter Bounds()"
Cohesion: 0.12
Nodes (14): Test validate_plot_save_path function., Test that None input returns None., Test valid PNG path is accepted., Test valid PDF path is accepted., Test valid SVG path is accepted., Test valid EPS path is accepted., Test valid JPG/JPEG paths are accepted., Test valid TIFF paths are accepted. (+6 more)

### Community 135 - "  Init  .Py / Get Device Status()"
Cohesion: 0.11
Nodes (23): _basic_correction_numpy(), _diagonal_correction_batch_jax(), _diagonal_correction_batch_numpy(), _diagonal_correction_jax(), _diagonal_correction_numpy(), _interpolation_correction_numpy(), _is_jax_array(), jit() (+15 more)

### Community 136 - "Time Grid() / Phi Angles()"
Cohesion: 0.08
Nodes (17): Integration Tests for Physics and Data Modules =================================, Create a complete XPCS configuration., Integration tests for data loading workflow., Test complete data loading workflow., Test that loaded data can be used in physics calculations., Test diagonal correction is properly applied to loaded data., Create a temporary directory for test files., Integration tests for data consistency across modules. (+9 more)

### Community 137 - "Get Xpcs Model() / Testmodelselection"
Cohesion: 0.08
Nodes (14): Tests for CMC configuration dataclass., Tests for param-aware shard sizing in get_num_shards., No significant adjustment when n_params = 7 (param_factor = 1.0)., Shard size scales up for n_params > 7., Shard size respects min_points_per_param floor., get_num_shards works without n_params for backward compatibility., More parameters results in larger shards (fewer shards)., Tests for reparameterization and bimodal config options. (+6 more)

### Community 138 - "Testdatavalidationedgecases / .Test Vali"
Cohesion: 0.14
Nodes (15): _apply_angle_filtering(), Core angle filtering logic shared by optimization and plotting.      This is a w, create_specific_angles_test_data(), Create test data with specific phi angles for targeted filtering tests.      Par, Test that no matching angles returns all angles (fallback)., Test that overlapping ranges don't create duplicate indices., Test filtering with very narrow range (single angle)., Test that lower bound is inclusive. (+7 more)

### Community 139 - "Testcorrelationdata / .Test C2 Maximum V"
Cohesion: 0.08
Nodes (15): create_disabled_filtering_config(), Create config with filtering disabled.      Returns     -------     dict, Test that MCMC uses all 9 angles when filtering is disabled., Unit tests for JAX array compatibility in angle filtering.  These tests ensure t, Test JAX array when all angles match filter., Verify that NumPy arrays still work correctly (backward compatibility)., Test angle filtering with NumPy arrays (baseline)., Baseline test with NumPy arrays. (+7 more)

### Community 140 - ".Format() / Constraintrule"
Cohesion: 0.1
Nodes (15): create_test_dataset(), DatasetMetadata, estimate_test_duration(), Large Dataset Mock Generators for NLSQ API Alignment Testing.  This module provi, Create mock XPCS dataset with specified dimensions.          Parameters, Generate synthetic XPCS correlation data.          Parameters         ----------, Create 1M point dataset (boundary: STANDARD → LARGE).          Dataset: 100 phi, Create 10M point dataset (boundary: LARGE → CHUNKED).          Dataset: 200 phi (+7 more)

### Community 141 - "Testangleinrange /  Angle In Range()"
Cohesion: 0.1
Nodes (17): get_default_parameters(), get_parameter_info(), parameter_bounds(), Physical Constants and Parameter Validation for Homodyne =======================, # NOTE: These are reference values. The PRIMARY bounds used by NLSQ/CMC, Get standard parameter bounds for all model types.      Returns:         Diction, Validate parameter values against bounds with tolerance.      This is the legacy, Get sensible default parameters for a model type.      Args:         model_type: (+9 more)

### Community 142 - ".Test Value And Grad() / .Test Forward M"
Cohesion: 0.1
Nodes (12): _compute_g1_total_core(), Compute total g1 correlation function as product of diffusion and shear.      Fo, Physics equivalence test between CMA-ES and NLSQ computation paths.  Validates t, Static mode (no shear) should be identical between both paths., g2 = offset + contrast * g1^2 should be identical before clipping.          Both, Verify NLSQ and CMA-ES produce identical g2 (no clipping in either path)., Test element-wise mode (used by CMA-ES for large data) vs meshgrid mode., Element-wise g1 values should match corresponding meshgrid entries.          CMA (+4 more)

### Community 143 - ".Test Linear Shear() / Calculate Shear R"
Cohesion: 0.15
Nodes (22): get_xla_mode_path(), Get the path for the XLA mode configuration file.      Uses the virtual environm, cleanup_completion_files(), cleanup_xla_activation_scripts(), cleanup_xla_config(), CleanupTarget, find_cleanup_targets(), get_venv_path() (+14 more)

### Community 144 - "Validate Args() / Testcliparameteroverri"
Cohesion: 0.11
Nodes (19): Compare g1_total (diffusion + shear) between CMC and NLSQ., Test diffusion computation parity between CMC and NLSQ., Verify trapezoid_cumsum produces same results as create_time_integral_matrix., Compare g1_diffusion between CMC element-wise and NLSQ meshgrid., TestCMCNLSQDiffusionComparison, _compute_g1_diffusion_meshgrid(), _compute_g1_shear_meshgrid(), _compute_g1_total_meshgrid() (+11 more)

### Community 145 - ".Test Case Insensitive() / Normalize Ana"
Cohesion: 0.11
Nodes (17): get_all_param_names(), get_bounds(), get_defaults(), get_param_names(), get_registry(), ParameterInfo, Parameter Registry for Homodyne Analysis  Centralized parameter registry that el, Get all parameter names including per-angle scaling.          Parameters (+9 more)

### Community 146 - "Test Nlsq Saving.Py / Testsavenlsqnpzfil"
Cohesion: 0.09
Nodes (15): Tests for ReparamConfig dataclass., Default config enables D_ref and gamma_ref transforms., Backward-compatible properties map to new names., Config can selectively disable transforms., Config stores custom t_ref., Tests for nlsq_prior_width_factor default change., Default width factor should be 2.0 (not 3.0)., from_dict uses 2.0 default. (+7 more)

### Community 147 - "Testoptimizationresult / .Test Result Ha"
Cohesion: 0.09
Nodes (14): Result of parameter validation with detailed error reporting.      Provides comp, String representation for logging., ValidationResult, Test edge cases for TheoryEngine., g1 should return correct shape for static mode., g1 should return correct shape for laminar flow mode., estimate_computation_cost should return comprehensive dict., Computation cost should scale with data size. (+6 more)

### Community 148 - "Testnlsqconfigfromdict / .Test From Empt"
Cohesion: 0.09
Nodes (12): Tests for correlation data extraction per TEST_REGENERATION_PLAN.md.      Tests:, Test c2 diagonal properties (t1 = t2)., Test c2 symmetry (c2[t1,t2] ≈ c2[t2,t1])., Test c2 decay behavior with time lag., Test c2 minimum value constraint., Test c2 maximum value constraint., Test c2 extraction preserves shape., Test c2 normalization to expected range. (+4 more)

### Community 149 - "Config.Py / Hardwareconfig"
Cohesion: 0.09
Nodes (12): Expanded gradient computation tests per TEST_REGENERATION_PLAN.md.      Tests: F, Test forward-mode automatic differentiation (jvp)., Test reverse-mode automatic differentiation (grad)., Test Jacobian matrix computation., Test gradient of chi-squared objective function., Test simultaneous value and gradient computation., Test gradient through chain of computations (chain rule)., Test gradient through conditional (jnp.where). (+4 more)

### Community 150 - "Model.Py / Xpcs Model Averaged()"
Cohesion: 0.11
Nodes (18): Validate physics-based parameter constraints beyond simple bounds.          Chec, Fallback validation when physics_validators module not available., ConstraintRule, ConstraintSeverity, get_constraint_summary(), PhysicsViolation, Physics-Based Parameter Validators for XPCS Analysis  Registry-driven validation, Validate a single parameter against physics constraints.      Args:         para (+10 more)

### Community 151 - "  Init  .Py / Api: Cmc Module"
Cohesion: 0.13
Nodes (13): _angle_in_range(), Check if angle is in range, accounting for wrap-around at +/-180.      This is a, Tests for wrap-aware angle range checking., Test angle inside normal range (min <= max)., Test angle outside normal range., Test angle at minimum boundary of normal range., Test angle at maximum boundary of normal range., Test angle in upper section of wrapped range. (+5 more)

### Community 152 - "Samplingplan / Reparamconfig"
Cohesion: 0.11
Nodes (20): dispatch_command(), Dispatch command based on parsed CLI arguments.      Parameters     ----------, _build_mcmc_runtime_kwargs(), _configure_device(), _get_default_config(), _load_configuration(), Configuration handling for Homodyne CLI.  Manages device configuration, config f, Collect runtime kwargs for fit_mcmc_jax from CLI args and YAML config. (+12 more)

### Community 153 - "Main() / Namedtuple"
Cohesion: 0.13
Nodes (13): normalize_analysis_mode(), Resolve analysis mode, inferring from parameter counts if needed.      Args:, Tests for normalize_analysis_mode function., Test explicit static mode normalization., Test that static_isotropic is normalized to static., Test explicit laminar flow mode normalization., Test that mode comparison is case insensitive., Test inference of static mode from scalar parameter count. (+5 more)

### Community 154 - "Performance Benchmarks / .Test Vmap Corr"
Cohesion: 0.11
Nodes (14): calculate_shear_rate(), Calculate time-dependent shear rate using discrete evaluation.      Follows refe, Integration tests for physics calculations on real data structures., Test time integral matrix calculation with diffusion coefficient., Test shear rate calculation over time series., Test physics calculations with JAX array output., TestPhysicsCalculationIntegration, Test suite for calculate_shear_rate function. (+6 more)

### Community 155 - ".  Init  () / .Get Prior()"
Cohesion: 0.12
Nodes (13): r"""Safe UNNORMALIZED sinc function: sin(x) / x (NOT sin(πx) / (πx)).      This, safe_sinc(), sinc(0) should be 1, not nan or inf., sinc near zero should be close to 1., Test suite for safe_sinc (unnormalized sinc: sin(x)/x)., Test safe_sinc returns 1.0 at x=0., Test safe_sinc near zero returns ~1.0., Test safe_sinc at multiples of pi. (+5 more)

### Community 156 - "Physics Params() / Testcmcphysicsvalues"
Cohesion: 0.09
Nodes (12): Tests for OptimizationResult handling (10 tests)., TC-RESULT-001: Result contains optimized parameters., TC-RESULT-002: Result contains parameter uncertainties., TC-RESULT-003: Result contains covariance matrix., TC-RESULT-004: Covariance matrix is positive semi-definite., TC-RESULT-005: Result has convergence status., TC-RESULT-006: Result has chi-squared metrics., TC-RESULT-007: Result has iteration count. (+4 more)

### Community 157 - " Load Data() / Testdataloading"
Cohesion: 0.09
Nodes (12): Test parsing convergence settings from dict., Test parsing nested diagnostics section., Test parsing nested streaming section., Test parsing nested stratified section., Test parsing nested recovery section., Test parsing nested hybrid_streaming section., Test parsing x_scale_map from dict., Test that numeric values are properly converted to float. (+4 more)

### Community 158 - "Mock Parameter Space() / .Test Bounds Cl"
Cohesion: 0.12
Nodes (15): detect_hardware(), HardwareConfig, Hardware detection and configuration helpers for CMC. ==========================, Hardware configuration for CMC optimization.      This dataclass encapsulates al, Auto-detect hardware configuration for CMC optimization.      This function perf, Tests for Hardware Detection Module ======================================  **Up, Test multiprocessing backend recommendation for CPU-only., Test HardwareConfig dataclass. (+7 more)

### Community 159 - "Testdatavalidation / Test Sigma Is Posit"
Cohesion: 0.13
Nodes (13): Validate and optionally clip initial value to parameter bounds.      Parameters, validate_initial_value_bounds(), Tests for validate_initial_value_bounds function., Test that values within bounds are returned unchanged., Test that values below lower bound are clipped with margin., Test that values above upper bound are clipped with margin., Test that NaN values are reset to midpoint., Test that inf values are reset to midpoint. (+5 more)

### Community 160 - "Validate Experimental Setup() / .Test Va"
Cohesion: 0.11
Nodes (13): _diagonal_correction_jax_core(), Core JAX implementation of basic diagonal correction (JIT-compiled).          Al, Test that JAX backend function can be JIT-compiled.          Note: The unified a, Test JIT equivalence with realistic large matrix, Test gradient using finite differences, Test vectorization with vmap using internal JIT function, Test vmap over phi angle axis (realistic NLSQ usage pattern), Test consistency across CPU devices (+5 more)

### Community 161 - "Get Num Parameters() / Get Parameter Nam"
Cohesion: 0.15
Nodes (17): _base_cmc_config(), _make_tiny_dataset(), _mock_nlsq_result_laminar(), _mock_nlsq_result_static(), _MockParameterSpace, Integration tests for NLSQ→CMC warm-start pipeline with adaptive sampling.  Vali, Non-adaptive should preserve config defaults for warmup/samples., Adaptive laminar_flow should have higher minimums (more params). (+9 more)

### Community 162 - "Main() / Nlsqdata"
Cohesion: 0.13
Nodes (21): API: CLI, API: Core Module, API: NLSQAdapter, API: NLSQWrapper, API: TheoryEngine, CLI dispatch_command() Orchestrator, CLI Config Handling, CLI Data Pipeline (+13 more)

### Community 163 - " Infer Time Step() / Testcmctimestepinfe"
Cohesion: 0.14
Nodes (12): Validate experimental setup parameters for physical reasonableness.      Args:, validate_experimental_setup(), Test edge cases for experimental setup validation., Q values at typical boundaries should be valid., Q values outside typical range should fail validation., L values at typical boundaries should be valid., L values outside typical range should fail validation., Reasonable X-ray wavelengths should pass validation. (+4 more)

### Community 164 - "Fit Mcmc Jax() / Multi Angle Data()"
Cohesion: 0.1
Nodes (11): Tests for data validation per TEST_REGENERATION_PLAN.md.      Tests: Shape, dtyp, Test c2 shape validation., Test c2 dtype validation., Test c2 finiteness validation., Test c2 physical range validation., Test sigma shape matches c2., Test sigma is positive., Test phi range validation. (+3 more)

### Community 165 - ".Test Diagnostics() / .Test Reset Clears"
Cohesion: 0.11
Nodes (13): get_num_parameters(), get_parameter_names(), Get number of parameters for analysis mode.      Parameters     ----------     a, Get parameter names for specified analysis mode.      Parameters     ----------, Test parameter name constant definitions., Verify static mode has 5 parameters., Verify laminar flow mode has 9 parameters., Verify static parameter ordering. (+5 more)

### Community 166 - "Plot Ess() / Plot Pair()"
Cohesion: 0.15
Nodes (18): compute_gradient_norms(), compute_optimal_x_scale(), _create_residual_function(), diagnose_gradient_imbalance(), print_gradient_report(), Gradient Diagnostics for Parameter Scaling Optimization ========================, Compute gradient L2 norms for each parameter at given point.      Args:, Compute optimal x_scale map based on gradient norms.      The x_scale values are (+10 more)

### Community 167 - "Testgetsafeoutputdir / Get Safe Output D"
Cohesion: 0.1
Nodes (12): Integration Tests for NLSQ API Conversions =====================================, Verify loss_augment_fn is callable with correct signature., Verify iteration_callback is callable with correct signature., Verify empty dict when no layers are active., T036: Test NLSQConfig.to_workflow_kwargs()., Verify kwargs are valid for CurveFit., Verify values are correctly copied.          Note: NLSQ 0.6.3+ removed old workf, Verify max_iterations maps to max_nfev. (+4 more)

### Community 168 - "Testcpudetection / Benchmark Cpu Perform"
Cohesion: 0.1
Nodes (10): Lightweight configuration validation.          Checks for required sections and, T051: Log key configuration values at INFO level.          Logs analysis mode, d, T053: Log unusual but valid settings with impact warnings.          Warns about, Normalize configuration schema for backward compatibility.          Handles mult, Normalize analysis_mode to canonical lowercase form.          Handles case-insen, Validate config_version against package version.          Warns if config versio, Normalize experimental_data section.          Supports two formats:         1. T, Get default configuration structure.          T052: Logs default value applicati (+2 more)

### Community 169 - "Safe Exp() / Testsafeexp"
Cohesion: 0.14
Nodes (12): Test get_safe_output_dir function., Test that None creates default subdirectory in cwd., Test custom default subdirectory name., Test existing directory is returned as-is., Test new directory is created if it doesn't exist., Test nested directories are created., Test path traversal is rejected., Test that existing file raises error. (+4 more)

### Community 170 - "Normalize Nlsq Result() / Testnormalizen"
Cohesion: 0.14
Nodes (12): normalize_nlsq_result(), Normalize various NLSQ result formats to standard format.      NLSQ can return r, Tests for normalize_nlsq_result function., Test normalization of dict result format., Test normalization of dict result with popt key., Test normalization of (popt, pcov) tuple., Test normalization of (popt, pcov, info) tuple., Test normalization of object with x attribute. (+4 more)

### Community 171 - ".Test Single Angle Range() / Testanglefi"
Cohesion: 0.13
Nodes (12): Safe exponential to prevent overflow.      Args:         x: Input array, safe_exp(), exp at large negative values should approach zero but not underflow., Test suite for safe_exp function., Test safe_exp with normal input values., Test safe_exp clips large positive values to prevent overflow., Test safe_exp clips large negative values., Test safe_exp with custom max_val parameter. (+4 more)

### Community 172 - "Testnlsqconfigconstantscaling / .Test Co"
Cohesion: 0.14
Nodes (12): create_time_integral_matrix(), r"""Create time integral matrix using trapezoidal numerical integration.      Co, Test suite for create_time_integral_matrix function., Test output matrix has correct shape., Test diagonal elements are approximately zero., Test matrix is symmetric., Test all elements are non-negative., Test with constant input array. (+4 more)

### Community 173 - "Test Project Metadata() / Test Warning S"
Cohesion: 0.1
Nodes (11): Test constant scaling configuration (T013-T015)., T013: Test 'constant' is accepted as valid per_angle_mode., Test all per_angle_mode options are accepted., Test constant_scaling_threshold has default value of 3., T014: Test constant_scaling_threshold is parsed from dict., Test constant_scaling_threshold parsed alongside per_angle_mode., T015: Test threshold < 1 produces validation error., Test negative threshold produces validation error. (+3 more)

### Community 174 - "Core.Py /  Fmt Time()"
Cohesion: 0.1
Nodes (19): Unit tests for Sphinx documentation configuration.  Tests validate that docs/con, Test that MathJax 3 is properly configured., Test that conf.py can be loaded without import errors., Test that autodoc_mock_imports only contains expected optional dependencies., Test that the HTML theme is properly configured.      Note: Project uses furo th, Test that MyST parser extensions are properly configured., Test that project metadata is correctly configured., Test that expected warnings are suppressed. (+11 more)

### Community 175 - "Physics Nlsq.Py / Compute G2 Scaled()"
Cohesion: 0.12
Nodes (15): build_init_values_dict(), estimate_per_angle_scaling(), Estimate contrast and offset initial values for each phi angle.      Thin wrappe, Build complete initial values dictionary in sampling order.      CRITICAL: Param, Validate that init values dictionary keys match expected order.      This is a d, validate_init_values_order(), Tests for build_init_values_dict with different modes., Test individual mode creates per-angle contrast/offset params. (+7 more)

### Community 176 - "Shardgrid / Physics Cmc.Py"
Cohesion: 0.16
Nodes (19): generate_diagnostic_plots(), _is_scaling_var(), plot_autocorr(), plot_energy(), plot_ess(), plot_forest(), plot_pair(), plot_rank() (+11 more)

### Community 177 - "Testmodelphysics / Xpcs Model Scaled()"
Cohesion: 0.11
Nodes (16): from_dict(), Adaptive Relative Regularization for Anti-Degeneracy Defense.  This module imple, Convert value to float safely, returning default on failure.      Parameters, Convert value to int safely, returning default on failure.      Parameters     -, safe_float(), safe_int(), CollapseEvent, create_gradient_function_with_monitoring() (+8 more)

### Community 178 - ".Test Both Transforms() / .Test D Ref Tr"
Cohesion: 0.12
Nodes (12): _infer_time_step(), Infer time step from pooled t1/t2 arrays (seconds).      Uses the median positiv, Median positive delta from pooled times is returned., Single unique value should warn and fall back to 1.0., All-zero diffs should warn and fall back to 1.0., Test edge cases for time step inference., Uniform time spacing should be detected correctly., Non-uniform spacing should return median diff. (+4 more)

### Community 179 - "Api: Jax Backend / Data Handler Architec"
Cohesion: 0.14
Nodes (13): _apply_angle_filtering_for_plot(), Apply angle filtering to select specific angles for plotting.      This is a wra, create_angle_filtering_test_data(), Create test data specifically for angle filtering tests.      Parameters     ---, Consistency validation tests for angle filtering.  This module ensures that opti, Verify all methods return original data when filtering disabled., Verify consistency with very narrow range (single angle)., Verify consistency holds across different dataset sizes. (+5 more)

### Community 180 - "Test Uninstall.Py / Testremovehomodynebl"
Cohesion: 0.13
Nodes (13): compute_uncertainties(), QualityMetrics, Result Building Utilities for NLSQ Optimization.  This module provides utilities, Quality metrics for optimization results.      Attributes:         chi_squared:, Build the result dictionary.          Args:             residual_fn: Residual fu, # NOTE: OOC and hierarchical paths use different keys, Extract parameter uncertainties from covariance matrix.      Args:         covar, Tests for compute_uncertainties function. (+5 more)

### Community 181 - ".Test Output Shape() / .Test Small Matri"
Cohesion: 0.12
Nodes (9): Spawn persistent worker processes and wait for readiness.          Each worker s, Check if pool has active workers., Submit a task to the next available worker (round-robin).          Parameters, Block until a result is available.          Parameters         ----------, Check if results are available without blocking., Send shutdown sentinels and join all workers.          Parameters         ------, Persistent process pool for CMC shard dispatch.      Workers are spawned once, p, WorkerPool (+1 more)

### Community 182 - "Test Config Manager.Py / Testparameterna"
Cohesion: 0.13
Nodes (13): NumPyro model with non-centered parameterization for gradient balancing.      Th, NumPyro model with non-centered parameterization for gradient balancing.      Th, xpcs_model_scaled(), Structural tests for xpcs_model_scaled without running MCMC.      xpcs_model_sca, Test that xpcs_model_scaled is callable with correct arguments., Test laminar_flow mode includes additional parameters., Test parameters are sampled in NumPyro-required order., Scientific validation tests for physics consistency. (+5 more)

### Community 183 - ".Test Beta Out Of Range() / .Test Negati"
Cohesion: 0.16
Nodes (19): CMC NumPyro Model Specification, CMC Reparameterization (t_ref, log-space), CombinedModel (primary model), Diagonal Correction (C2 artifact removal), DiffusionModel, g1 Diffusion Contribution (exp formula), g1 Shear Contribution (sinc^2 formula), g2 Siegert Relation (homodyne) (+11 more)

### Community 184 - "Testworkerpool / .Test Worker Reuse()"
Cohesion: 0.16
Nodes (19): API: CMC Backends, API: CMC Module, ArviZ Diagnostics (R-hat, ESS, BFMI), CMC Fitting Architecture, CMC Auto Shard Size Selection, CMC Consensus Posterior Combination, CMC Data Preparation & Sharding, LPT Noise-Weighted Shard Scheduling (+11 more)

### Community 185 - ".Test Single Chunk() / .Test Identical R"
Cohesion: 0.16
Nodes (19): API: JAX Backend, ConfigManager (YAML/JSON config), Data Filtering Utils (Q-range, phi, quality), End-to-End Data Flow Pipeline, Data Handler Architecture, Data Preprocessing Pipeline, Data Validation (NaN, shape, range), Gradient-Safe Positivity Floor (jnp.where) (+11 more)

### Community 186 - "Nlsq Plots.Py / Generate Nlsq Plots()"
Cohesion: 0.2
Nodes (19): Anti-Degeneracy Defense (per-angle mode), AntiDegeneracyController (per-angle scaling), CMA-ES Global Optimizer, CMAESWrapper (global optimizer), CMA-ES Scale Ratio Trigger (scale ratio > 1e6 → CMA-ES), FallbackChain (OptimizationStrategy enum), fit_nlsq_jax() Function, Hybrid Streaming Strategy (>10M pts) (+11 more)

### Community 187 - "Commands.Py /  Save Results()"
Cohesion: 0.11
Nodes (10): TC-CORE-JAX-002: Test float32 dtype preservation., TC-CORE-JAX-003: Test float64 dtype preservation., TC-CORE-JAX-004: Test meshgrid creation for correlation functions., TC-CORE-JAX-005: Test jnp.linspace precision matches NumPy., TC-CORE-JAX-006: Test zeros/ones array creation., TC-CORE-JAX-007: Verify arrays are placed on a valid device.          Note: Whil, TC-CORE-JAX-008: Test reshape operations preserve data., Tests for JAX array creation and dtype handling per TEST_REGENERATION_PLAN.md. (+2 more)

### Community 188 - "Log Exception() / Testlogexception"
Cohesion: 0.11
Nodes (10): Test WARNING for alpha > 1.0., Test WARNING for negative D_offset., Test WARNING for gamma_dot_t0 > 0.5., Test WARNING for beta outside [-2, 2]., Test that small negative gamma_dot_t_offset is now valid (within bounds)., Test WARNING for contrast < 0.1., Test WARNING-level physics violations (unusual but possible)., Test WARNING for D0 > 1e7. (+2 more)

### Community 189 - "Test Api Documentation.Py / Test Core Mo"
Cohesion: 0.11
Nodes (11): Unit tests for configuration parameter management.  Tests for ParameterManager,, Tests for parameter name mapping and extraction., Test extracting base name from indexed contrast parameter., Test extracting base name from indexed offset parameter., Test extracting base name from non-indexed parameter returns None., Test invalid indexed parameter patterns return None., Tests for parameter bounds ordering consistency., Test that bounds for static mode maintain consistent ordering. (+3 more)

### Community 190 - "Standardexecutor / Teststandardexecutor"
Cohesion: 0.17
Nodes (12): accumulate_chunks_parallel(), accumulate_chunks_sequential(), Accumulate chunk results sequentially.      Parameters     ----------     chunks, Accumulate chunk results in parallel via process pool.      Partitions chunks ac, Test parallel with n_workers > n_chunks (sparse partitioning)., Test n_workers=0 falls back to sequential., Test that parallel == sequential accumulation., Core correctness: parallel accumulation == sequential. (+4 more)

### Community 191 - "Get Executor() / Testgetexecutor"
Cohesion: 0.11
Nodes (11): Unit tests for enhanced logging APIs.  Tests for: - T006: with_context() - T007:, T025: Tests for numerical error logging with context., NaN detection logs iteration, parameter values, and context., Inf detection logs residual info and context., Bounds violation logs before/after parameter values., T042: Tests for with_context() shard ID formatting., with_context(shard=id) adds shard prefix to log messages., with_context supports multiple keys. (+3 more)

### Community 192 - "Testjaxarraycreation / .Test Meshgrid Cr"
Cohesion: 0.11
Nodes (10): T009: Tests for LogConfiguration dataclass., Default configuration values are correct., Configuration created from dictionary., --verbose flag sets DEBUG console level., --quiet flag sets ERROR console level., --log-file sets file path., quiet takes precedence over verbose., apply() returns log file path when file logging enabled. (+2 more)

### Community 193 - "Testparameterboundsdetection /  Classify"
Cohesion: 0.14
Nodes (11): Remove homodyne-injected blocks from activate script content.      Uses a line-b, _remove_homodyne_blocks(), Tests for uninstall_scripts._remove_homodyne_blocks state machine.  Validates: -, Block with missing end marker: header + body lines are stripped to EOF., Tests for the state-machine block remover., Single completion block with fi terminator is removed., Single fish block with end terminator is removed., Both completion and XLA blocks removed from one file. (+3 more)

### Community 194 - "Abc / Fit()"
Cohesion: 0.11
Nodes (17): Unit tests for API documentation generation.  Tests validate that Sphinx autodoc, Test that API reference RST files will be created., Test that autosummary can generate module stubs.      This is a slow test that a, Test that autodoc can import homodyne package without errors., Test that type hints are accessible for autodoc., Test that core submodules can be imported., Test that optimization submodules can be imported., Test that config module can be imported. (+9 more)

### Community 195 - "Testvalidateinput / Nan In T1 Raises Val"
Cohesion: 0.12
Nodes (10): ABC, NLSQAdapterBase, Abstract base class for NLSQ adapters (FR-012).  Provides shared methods for NLS, Validate input arrays for consistency.          Parameters         ----------, Build standardized result dictionary.          Parameters         ----------, Abstract base class for NLSQ optimization adapters.      Provides shared methods, Handle optimization errors gracefully.          Parameters         ----------, Setup parameter bounds arrays.          Parameters         ----------         pa (+2 more)

### Community 196 - "Testnlsqwrapperinit / .Test Wrapper Init"
Cohesion: 0.11
Nodes (10): Tests for _validate_input() method., Valid input passes validation without error., Mismatched t1 and t2 lengths raise ValueError., Mismatched phi length raises ValueError., Mismatched g2 length raises ValueError., NaN in t1 raises ValueError., Inf in g2 raises ValueError., Empty arrays raise ValueError. (+2 more)

### Community 197 - "Testconsistentperangleinit / . Create Mo"
Cohesion: 0.15
Nodes (11): get_executor(), Factory function to get the appropriate executor.      Args:         strategy_na, Tests for get_executor factory function., Test getting standard executor., Test getting large dataset executor., Test that chunked strategy maps to large executor., Test getting streaming executor., Test getting streaming executor with config. (+3 more)

### Community 198 - "Testnlsqconfigdefaults / .Test Default L"
Cohesion: 0.15
Nodes (12): Standard curve_fit optimization for small datasets (<1M points).      Uses scipy, StandardExecutor, Tests for x_scale parameter handling in executors., Test StandardExecutor with scalar x_scale., Test StandardExecutor with array x_scale., Test StandardExecutor with 'jac' x_scale., Tests for StandardExecutor class., Test StandardExecutor name property. (+4 more)

### Community 199 - "Testcmcconfigperanglemode / .Test Defaul"
Cohesion: 0.13
Nodes (11): Unit Tests for NLSQ Validation Utilities =======================================, Tests for validate_bounds_consistency function., Consistent bounds pass., Bounds with wrong length fail., TestValidateBoundsConsistency, Input validation for NLSQ optimization (T079).  Extracted from wrapper.py as par, Validate that bounds are consistent.      Parameters     ----------     bounds :, Validate that initial parameters are within bounds.      Parameters     -------- (+3 more)

### Community 200 - ".Test Inf In C2() / .Test Nan In C2()"
Cohesion: 0.11
Nodes (10): Test suite for apply_diagonal_correction function., Test output has same shape as input., Test that diagonal values are modified., Test that off-diagonal elements are unchanged., Test edge elements (first and last diagonal) are handled correctly., Test symmetric input produces symmetric output., Test with 2x2 matrix (minimum size)., Test output contains only finite values. (+2 more)

### Community 201 - "Enable D Total() / Enable Log Gamma()"
Cohesion: 0.16
Nodes (17): get_optimal_batch_size(), Calculate optimal batch size for CPU processing.      Parameters     ----------, Calculate optimal batch size for CPU processing.      Parameters     ----------, benchmark_and_report(), configure_cpu_optimal(), detect_hpc_environment(), generate_synthetic_xpcs_data(), main() (+9 more)

### Community 202 - "Testcmcresult / .Test Ess Values()"
Cohesion: 0.14
Nodes (10): TC-INIT-004: Static mode should also work (no shear parameters)., TC-INIT-005: Should fall back to defaults if fitting fails., TC-INIT-006: Zero shear rate should behave like static mode., TC-INIT-007: Verify the condition for triggering consistent init.          The c, Tests for _compute_consistent_per_angle_init function.      These tests verify t, Create mock stratified data for testing., TC-INIT-001: Function returns arrays with correct shape., TC-INIT-002: Returned values should be within reasonable physical bounds. (+2 more)

### Community 203 - "Testcmcresultvalidation / .Test Validate"
Cohesion: 0.11
Nodes (10): Test NLSQConfig default values., Test default loss function is soft_l1., Test default convergence tolerances., Test default scaling settings., Test diagnostics enabled by default., Test default streaming optimizer settings., Test default stratified optimization settings., Test default recovery settings. (+2 more)

### Community 204 - "Testcmcconfig / .Test Default Values()"
Cohesion: 0.11
Nodes (10): Tests for CMCResult dataclass., Test is_cmc_result returns True., Test success property returns True when converged., Test success property returns False when not converged., Test success property returns False with divergences., Test param_names is a list., Test samples dict has correct structure., Test ESS contains values for all parameters. (+2 more)

### Community 205 - "Get Template Path() / Testgettemplatepat"
Cohesion: 0.11
Nodes (10): Tests for CMCResult.validate_parameters method., Test validation passes for complete static result., Test validation catches missing physical parameter., Test validation catches non-finite values., Test validation warns about high R-hat., Test validation warns about low ESS., Test validation warns about high divergence rate., Test validation can infer n_phi from sample names. (+2 more)

### Community 206 - ".Test From Dict() / Testlogconfiguration"
Cohesion: 0.11
Nodes (10): Test submitting tasks and collecting results., Test that a single worker handles multiple tasks., Test that worker errors are captured, not lost., Test WorkerPool as context manager., Test that calling shutdown() twice is safe., Test that worker_init_fn is called once per worker before tasks., Test that worker_fn returning None does not put on result queue., Test that result_queue property returns the internal queue. (+2 more)

### Community 207 - "Test Logging.Py / Testwithcontextshard"
Cohesion: 0.14
Nodes (11): Tests for parameter bounds and shear collapse detection.      These tests verify, TC-BOUNDS-001: All parameters within bounds should be 'active'., TC-BOUNDS-002: Parameter at lower bound should be detected., TC-BOUNDS-003: Parameter at upper bound should be detected., TC-BOUNDS-004: No bounds should return all 'active'., TC-BOUNDS-005: Value near but not at bound should be 'active'., TC-BOUNDS-006: Verify shear collapse detection threshold., TC-BOUNDS-007: Verify laminar_flow parameter ordering for bounds check. (+3 more)

### Community 208 - ".Submit() / Workerpool"
Cohesion: 0.15
Nodes (11): Validate that model output is physically reasonable.      Parameters     -------, validate_model_output(), Tests for validate_model_output function., Test validation passes for valid output., Test validation fails for NaN values., Test validation fails for infinite values., Test validation fails for negative C2 (unphysical)., Test validation fails for very high C2 values. (+3 more)

### Community 209 - "Fallback Chain.Py /  Get Strategy Info()"
Cohesion: 0.11
Nodes (10): Tests for per_angle_mode in CMCConfig., Verify default per_angle_mode is 'auto'., Test parsing per_angle_mode from config dict., Test auto mode returns 'auto' when n_phi >= threshold.          When n_phi >= th, Test auto mode selects individual when n_phi < threshold., Test explicit mode selection overrides auto logic., Test to_dict includes per_angle_mode fields., Test validation rejects invalid per_angle_mode values. (+2 more)

### Community 210 - "Main() / Print Usage Guide()"
Cohesion: 0.15
Nodes (11): get_template_path(), Get template file path for given mode.      Parameters     ----------     mode :, Tests for get_template_path function., Test getting template path for static mode., Test getting template path for laminar_flow mode., Test that template files actually exist., Test that invalid mode raises KeyError., Test that returned path is absolute. (+3 more)

### Community 211 - "Main() / Cpu Optimization.Py"
Cohesion: 0.11
Nodes (10): Tests for NLSQWrapper initialization (8 tests)., TC-WRAPPER-001: Initialize wrapper with default parameters., TC-WRAPPER-002: Initialize with large dataset support disabled., TC-WRAPPER-003: Initialize with error recovery disabled., TC-WRAPPER-004: Initialize with custom max retries., TC-WRAPPER-005: Initialize with fast mode enabled., TC-WRAPPER-006: Per-angle scaling is mandatory in v2.4.0+., TC-WRAPPER-007: Initialize with numerical validation disabled. (+2 more)

### Community 212 - "Name() / Execute()"
Cohesion: 0.15
Nodes (16): _compute_g1_diffusion_from_idx(), _compute_g1_shear_elementwise(), _compute_g1_shear_from_idx(), compute_g1_total(), _compute_g1_total_elementwise(), _compute_g1_total_with_precomputed(), CMC Physics Backend - Element-wise Computations Only ===========================, Diffusion g1 using pre-computed indices and time_safe.      Replaces ``_compute_ (+8 more)

### Community 213 - ".  Init  () / .Snapshot()"
Cohesion: 0.13
Nodes (14): execute_optimization_with_fallback(), get_fallback_strategy(), _get_strategy_info(), handle_nlsq_result(), OptimizationStrategy, Fallback chain logic for NLSQ optimization strategy selection.  Extracted from w, Execute optimization with strategy fallback.      Tries selected strategy first,, Local optimization strategy enum for internal use.      Note: This replaces the (+6 more)

### Community 214 - ".Apply() / .Format()"
Cohesion: 0.15
Nodes (9): MinimalLogger, Apply this configuration to the logging system.          Returns:             Pa, Convert string/int log level to logging level constant., Configurable logger manager for the homodyne package.      Thread-safe singleton, Configure homodyne logging.          Thread-safe configuration of the logging sy, Internal implementation of configure (called under lock)., Configure logging from a `logging:` config section., Get or create a logger with hierarchical naming. (+1 more)

### Community 215 - "Shearmodel / Diffusionmodel"
Cohesion: 0.18
Nodes (12): benchmark_diagonal_correction_memory(), benchmark_optimization_memory(), get_memory_mb(), MemoryProfiler, Get current process memory usage in MB., Track memory usage during optimization iterations.      Performance Optimization, Take memory snapshot with label., Set baseline memory (call before operation). (+4 more)

### Community 216 - ".Test Zeros Matrix() / .Test Uniform Val"
Cohesion: 0.16
Nodes (16): demonstrate_dynamic_worker_scaling(), generate_multiple_datasets(), main(), parallel_batch_processing(), print_batch_results(), print_usage_guide(), process_single_dataset(), Process a single XPCS dataset with NLSQ optimization.      This function runs in (+8 more)

### Community 217 - "Testconfigloadingedgecases / .Test Load "
Cohesion: 0.12
Nodes (12): Test that CPU info includes architecture details., Test that configure_cpu_hpc returns configuration dict., Test CPU configuration with hyperthreading enabled., Test that configure_cpu_hpc returns configuration dict., Test CPU configuration with different NUMA policies., Test CPU configuration with different memory optimization levels., Test CPU configuration with hyperthreading enabled., Test CPU configuration with different NUMA policies. (+4 more)

### Community 218 - "Testparameterexpansion / .Test Bounds Ex"
Cohesion: 0.12
Nodes (10): Direct comparison test between CMC and NLSQ physics computations.  This test ver, Test that searchsorted correctly maps physical times to grid indices., Verify searchsorted finds exact matches correctly., Verify searchsorted behavior for values between grid points., Verify cumsum integral computation for specific time pairs., Test that CMC physics produces physically reasonable values., Verify g1 decays to small values at large time separations., Debug test to check physics prefactor magnitudes. (+2 more)

### Community 219 - "Test With Infinity Values. / Testinvalid"
Cohesion: 0.14
Nodes (11): Save posterior samples in ArviZ-compatible format.      The saved file can be lo, save_samples_npz(), Tests for CMC I/O module., Test save creates npz file., Test saved file contains all required fields., Test posterior_samples has correct shape., Tests for save/load round-trip consistency., Test save then load preserves all data. (+3 more)

### Community 220 - "Testparameterspacefromconfig / .Test Loa"
Cohesion: 0.13
Nodes (14): _populate_reparam_priors(), Populate reparameterized prior values in nlsq_prior_config.      This is deferre, Transform NLSQ estimates to reference-time reparameterized space.      Computes, Transform NLSQ estimates to reference-time reparameterized space.      Computes, transform_nlsq_to_reparam_space(), Tests for transform_nlsq_to_reparam_space function., Transforms NLSQ values to reparameterized space., Delta-method uncertainty propagation works. (+6 more)

### Community 221 - ".Test Static Params Count() / .Test Scal"
Cohesion: 0.14
Nodes (16): _cap_laminar_max_points(), _compute_suggested_timeout(), _estimate_n_workers(), _fmt_time(), _log_runtime_comparison(), _log_runtime_estimate(), CMC core module - main entry point.  This module provides the fit_mcmc_jax() fun, Simplified interface for CMC analysis.      This is a convenience wrapper around (+8 more)

### Community 222 - "Test Error For D0 = 0. / .Test Multiple "
Cohesion: 0.12
Nodes (9): Test edge cases for parameter validation functions., Empty parameter arrays should fail validation., Mismatched parameter count should fail with descriptive error., Parameters exactly at bounds should be valid., Parameters slightly outside bounds should respect tolerance., NaN parameters should fail validation., Infinite parameters should fail validation., ValidationResult should format messages correctly. (+1 more)

### Community 223 - "Testt0Exclusion /  Exclude T0 From Analy"
Cohesion: 0.12
Nodes (9): JSON config should be usable in same structure as YAML., Test edge cases for configuration loading., Loading non-existent file should raise XPCSConfigurationError., Loading unsupported format should raise XPCSConfigurationError., Loading invalid YAML should raise XPCSConfigurationError., Loading invalid JSON should raise XPCSConfigurationError., Loading empty YAML should return None or empty dict., YAML with anchors should be parsed correctly. (+1 more)

### Community 224 - ".  Init  () / Inputvalidator"
Cohesion: 0.12
Nodes (9): Test parameter expansion for per-angle scaling., Test basic parameter expansion for 3 angles., Test parameter expansion for static_mode mode., Test that physical parameters are preserved exactly., Test the parameter count formula for various angle counts., Test that bounds are expanded correctly., Test that parameter ordering matches StratifiedResidualFunction expectations., Test that parameter count validation detects mismatches. (+1 more)

### Community 225 - ".Validate All() / Input Validator.Py"
Cohesion: 0.12
Nodes (9): Test ERROR-level physics violations (physically impossible)., Test ERROR for negative D0., Test ERROR for D0 = 0., Test ERROR for negative gamma_dot_t0., Test ERROR for contrast > 1., Test ERROR for contrast = 0., Test ERROR for negative offset., Test multiple ERROR violations. (+1 more)

### Community 226 - ".  Repr  () / Homodynemodel"
Cohesion: 0.12
Nodes (9): Tests for static vs laminar_flow parameter sets., Test that static params are subset of laminar_flow params., Test number of static parameters., Test number of laminar_flow parameters., Test number of scaling parameters., Test that static params contain expected parameters., Test that laminar_flow params contain expected parameters., Test that scaling params contain contrast and offset. (+1 more)

### Community 227 - "Trapezoid Cumsum() / Testtrapezoidcumsum"
Cohesion: 0.17
Nodes (10): compute_scaling_factors(), Compute scaling factors for all parameters.      Parameters     ----------     p, Test that static mode creates scaling for correct parameters., Test that scaling factors use bounds from parameter space., Test that all scales are positive., Test that scale has minimum value of 1e-6., Test that scaling works when get_prior raises KeyError., Tests for compute_scaling_factors function. (+2 more)

### Community 228 - "Testmethodargumentparsing / .Test Method"
Cohesion: 0.12
Nodes (9): Tests for ParameterSpace.from_config() class method., Test loading valid static configuration., Test loading valid laminar flow configuration., Test loading config with missing bounds section (uses defaults)., Test loading config with partial bounds (missing some parameters)., Test loading config without parameter_space section (uses defaults)., Test automatic detection of analysis mode from config., Test that explicit analysis_mode parameter overrides config. (+1 more)

### Community 229 - ".Test Good Quality Fit() / .Test Poor Qu"
Cohesion: 0.12
Nodes (9): Test NLSQ → MCMC workflow for laminar flow mode., Test MCMC with some parameters fixed from NLSQ.          User might want to:, Test MCMC on active parameter subset.          Different from fixed_parameters:, Test exploration mode without NLSQ results.          User might want to run MCMC, Test realistic workflow simulating NLSQ → MCMC transition.          Simulates:, Test that ConfigManager integrates correctly with ParameterManager.          Ver, Test config-driven MCMC initialization workflow., Test NLSQ → MCMC workflow for static mode.          Workflow:         1. User ru (+1 more)

### Community 230 - "Testnlsqadapterbase / .Test Adapter Base"
Cohesion: 0.12
Nodes (9): Test loading of per-angle scaling parameters (contrast, offset) from config.  Th, Test config with only contrast specified in per_angle_scaling., Test suite for per-angle scaling parameter loading., Test config with only offset specified in per_angle_scaling., Test loading scalar contrast and offset for single-angle analysis., Test with realistic values from Simon's configuration., Test loading per-angle contrast and offset for multi-angle analysis., Test that config without per_angle_scaling still works. (+1 more)

### Community 231 - ".Test Wavevector T1 T2 Unchanged() / .Te"
Cohesion: 0.12
Nodes (9): Tests for T057: NLSQAdapterBase interface., Test that NLSQAdapterBase ABC exists and has required methods., Test that _prepare_data method exists and is callable., Test that _validate_input method exists and is callable., Test that _build_result method exists and is callable., Test that _handle_error method exists and is callable., Test that _setup_bounds method exists and is callable., Test that _compute_covariance method exists and is callable. (+1 more)

### Community 232 - "Testnlsqconfigtodict / .Test To Dict Rou"
Cohesion: 0.16
Nodes (10): Tests for InputValidator class., Valid data passes all validation., Mismatched dimensions are rejected., NaN in xdata is rejected., Non-strict mode returns False but doesn't raise., Initial params outside bounds are rejected., TestInputValidator, InputValidator (+2 more)

### Community 233 - "Parameterscaling / Testparameterscaling"
Cohesion: 0.17
Nodes (10): HomodyneModel, Hybrid architecture wrapper for homodyne XPCS analysis.      This class combines, String representation of HomodyneModel., Test that missing configuration keys raise appropriate errors., Test HomodyneModel initialization and configuration extraction., Test initialization with laminar flow configuration., Test initialization with static mode configuration., Test that physics factors are pre-computed at initialization. (+2 more)

### Community 234 - ".  Init  () / .Get Prior()"
Cohesion: 0.17
Nodes (10): Test _sanitize_log_path function., Test short paths pass through unchanged., Test newlines are escaped to prevent log injection., Test carriage returns are escaped., Test that long paths are truncated., Test truncation shows beginning and end of path., Test custom max_length parameter., TestSanitizeLogPath (+2 more)

### Community 235 - "Mock Parameter Space() / .Test Transform"
Cohesion: 0.12
Nodes (8): Pre-compute GLOBAL unique values from ALL chunks to avoid jnp.unique() in JIT., Compute flat indices for mapping chunk points to global grid positions., Pre-compile JAX functions for performance.          This method sets up JIT-comp, Pre-convert chunk arrays to JAX arrays during initialization.          This avoi, Concatenate all chunk data into single arrays for device-side iteration., Run chunk-structure validation while self.chunks is still available.          Ca, Initialize the stratified residual function.          Args:             stratifi, Create vmap-wrapped g2 computation functions once during init.          Avoids r

### Community 236 - "Testvalidateplotarrays / .Test Names Opt"
Cohesion: 0.12
Nodes (9): Edge case tests for diagonal correction, Test with minimum valid matrix size 2x2, Test with large 1000x1000 matrix, Test with identity matrix, Test with all-zeros matrix, Test with matrix of uniform values, Test numerical stability with large diagonal values, Test numerical stability with very small off-diagonal values (+1 more)

### Community 237 - ".Test All Inf Array() / Test Viz Validat"
Cohesion: 0.12
Nodes (9): Test that --method cmc is accepted and triggers automatic selection., Test that --method nuts raises clear error message., Test that --method mcmc raises clear error message (use cmc instead)., Test that --method auto raises clear error message., Test that default method is nlsq when not specified., Test that method choices are restricted to nlsq and cmc only., Test CLI method argument parsing after simplification., Test that --method nlsq is accepted. (+1 more)

### Community 238 - "Configmanager / Homodynemodel"
Cohesion: 0.17
Nodes (10): compute_quality_metrics(), Compute quality metrics from residuals.      Args:         residuals: Array of r, Test that marginal quality flag is assigned correctly., Test that division by zero is avoided when n_data == n_params., Tests for compute_quality_metrics function., Test quality metrics for a good fit., Test quality metrics for a poor fit., Test quality metrics with parameters at bounds. (+2 more)

### Community 239 - "Configuration Index / Configure Cpu Hpc("
Cohesion: 0.16
Nodes (14): _json_safe(), Save optimization results to output directory.      Parameters     ----------, Convert nested objects to JSON-serializable primitives.      This is a wrapper t, _save_results(), create_mcmc_analysis_dict(), create_mcmc_diagnostics_dict(), create_mcmc_parameters_dict(), _get_parameter_names() (+6 more)

### Community 240 - "Test Workflows.Py / Testendtoendworkflow"
Cohesion: 0.12
Nodes (10): Unit tests for device detection and configuration.  Tests for CPU detection, dev, Tests for module exports and API., Test that benchmark results include test size., Test that configure_optimal_device is exported., Test that get_device_status is exported., Tests for module exports and API., Test that HAS_CPU_MODULE flag is defined., Test that configure_optimal_device is exported. (+2 more)

### Community 241 - ".  Init  () / Resultvalidator"
Cohesion: 0.13
Nodes (12): main(), Main benchmark function., Run CPU benchmark with or without oneDNN.      Args:         enable_onednn: Whet, run_benchmark(), detect_cpu_info(), Detect CPU architecture and capabilities for optimization.      Returns     ----, Test that CPU info includes NUMA node count., Test that CPU info includes NUMA node count. (+4 more)

### Community 242 - "Nlsqadapter / Nlsqwrapper"
Cohesion: 0.17
Nodes (10): Cumulative trapezoid integral without dt scaling (dt is applied outside).      R, trapezoid_cumsum(), Test suite for trapezoid_cumsum function., Test output has same length as input., Test cumsum starts at zero., Test with constant input., Test with linear input., Test with single element: no intervals, so cumulative integral is [0.0]. (+2 more)

### Community 243 - "Testhdf5Formatdetection / .Create Mock A"
Cohesion: 0.12
Nodes (9): Test NLSQConfig.to_dict method., Test to_dict includes all configuration fields., Test diagnostics section structure., Test streaming section structure., Test stratified section structure., Test recovery section structure., Test hybrid_streaming section structure., Test that to_dict -> from_dict preserves values.          Note: ftol in to_dict (+1 more)

### Community 244 - "Clip Parameters() / Testclipparametersed"
Cohesion: 0.17
Nodes (10): ParameterScaling, Scaling parameters for a single parameter.      Attributes     ----------     na, Tests for ParameterScaling dataclass., Test that center maps to z=0., Test that center + scale maps to z=1., Test that center - scale maps to z=-1., Test that z=0 maps to center., Test that to_original stays within bounds. (+2 more)

### Community 245 - "Testcombinedmodeledgecases / .Test Compu"
Cohesion: 0.15
Nodes (9): ParameterRegistry, Singleton pattern - return existing instance if available., Get parameter metadata.          Parameters         ----------         name : st, Get physical parameter names for analysis mode.          Parameters         ----, Get parameter bounds.          Parameters         ----------         name : str, Get default values for all parameters.          T055: Logs parameter initial val, Expand scalar scaling values to per-angle parameters.          Parameters, Normalize analysis mode string. (+1 more)

### Community 246 - "Validate Parameter Names() / Testparamet"
Cohesion: 0.15
Nodes (12): mock_parameter_space_laminar(), mock_parameter_space_static(), MockParameterSpace, MockPriorSpec, Tests for CMC NumPyro model module.  Comprehensive tests for: - xpcs_model_scale, Mock PriorDistribution-like object., Mock ParameterSpace for testing without full config system., Mock ParameterSpace for static mode. (+4 more)

### Community 247 - "Testparameterbounds / .Test Get Bounds A"
Cohesion: 0.12
Nodes (9): Arrays with no NaN/Inf should return True., Arrays with NaN should return False and log warning., Arrays with Inf should return False and log warning., Mix of clean and dirty arrays should return False., Empty arrays should be considered clean., Should work without names parameter., No arrays should return True (vacuously)., Tests for validate_plot_arrays utility. (+1 more)

### Community 248 - ".Test All Active() / .Test At Lower Boun"
Cohesion: 0.12
Nodes (9): Unit tests for visualization validation utilities.  Tests for pre-plot data vali, Tests for validate_plot_arrays function., Test validation of single NaN element., Test with explicit None for names parameter., Test that multiple clean arrays return True., Test that arrays with Inf return False., Test array with all NaN values., Test array with both NaN and Inf values. (+1 more)

### Community 249 - "Testadaptivechunksize / .Test No Angles "
Cohesion: 0.13
Nodes (9): _OptimizeResult, Create physical loss function with pre-allocated buffer (FR-002).          Uses, Create physical gradient function with pre-allocated buffer (FR-002).          U, Create per-angle loss function with pre-allocated buffer (FR-002).          Uses, Create per-angle gradient function with pre-allocated buffer (FR-002)., Run hierarchical optimization.          Parameters         ----------         lo, Stage 1: Optimize physical parameters with per-angle frozen.          Performanc, Stage 2: Optimize per-angle parameters with physical frozen.          Performanc (+1 more)

### Community 250 - " Ooc Worker Init() / Create Ooc Kernels("
Cohesion: 0.12
Nodes (10): create_overlapping_ranges_config(), Create config with overlapping angle ranges.      Tests that angles matching mul, Edge case integration tests for optimization with angle filtering.  This module, Test that filtering edge cases maintain system stability., Edge case integration tests for optimization with filtering., Test NLSQ with no matching angles falls back to all angles., Test overlapping ranges produce no duplicate angles in full workflow., Test MCMC with no matching angles falls back to all angles. (+2 more)

### Community 251 - ".  Init  () / . Get Colormap()"
Cohesion: 0.15
Nodes (10): create_anisotropic_filtering_config(), Create phi_filtering config for anisotropic analysis.      Includes 2 ranges: pa, Test the _apply_angle_filtering_for_optimization() wrapper function., Test filtering enabled with angles that match ranges., Test that filtered data dict preserves all required keys., Test that C2 data first dimension is sliced correctly., Test that wavevector_q_list, t1, t2 remain unchanged., Test that function works with ConfigManager objects. (+2 more)

### Community 252 - "Validate Covariance() / Testvalidatecova"
Cohesion: 0.12
Nodes (9): Test numerical validation at 3 critical points., Test NaN detection in gradients., Test Inf detection in gradients., Test NaN detection in parameters., Test parameter bounds validation., Test NaN detection in loss values., Test Inf detection in loss values., Test that validation identifies which point failed. (+1 more)

### Community 253 - ".Validate All() / Nan Chi-Squared Fails."
Cohesion: 0.17
Nodes (16): CMC Fitting Architecture (arch doc), CMC data_prep.py (sharding, validation, noise estimation), CMC diagnostics.py (R-hat, ESS, bimodal detection), CMC model.py (5 NumPyro model variants), CMC priors.py (NLSQ-informed priors), CMC Reparameterization API Doc, CMCResult (posterior + diagnostics), CMC results.py (CMCResult dataclass) (+8 more)

### Community 254 - "Finite Parameters Pass. / .Test Inf Para"
Cohesion: 0.13
Nodes (11): Integration Tests for Scientific Workflows =====================================, Test interaction between different modules., Test configuration manager integration with other modules., Test cross-platform compatibility and behavior., Test consistent path handling across platforms., Test numerical precision consistency across platforms., Test complete end-to-end analysis workflows., test_yaml_config_workflow() (+3 more)

### Community 255 - "Testcmcargumentparsing / .Test Cmc Backe"
Cohesion: 0.16
Nodes (9): Tests for validate_result_consistency function., Valid chi-squared passes., NaN chi-squared fails., Inf chi-squared fails., Negative chi-squared fails., TestValidateResultConsistency, Result validation for NLSQ optimization (T080).  Extracted from wrapper.py as pa, Validate consistency of optimization result.      Parameters     ---------- (+1 more)

### Community 256 - "Optimization Runner.Py /  Run Nlsq Optim"
Cohesion: 0.16
Nodes (13): configure_cpu_hpc(), configure_cpu_threading(), _configure_jax_cpu(), HPC CPU Optimization for Homodyne ====================================  CPU-prim, Configure JAX and system for HPC CPU optimization.      Optimizes thread allocat, Set environment variables for optimal CPU performance., Configure JAX for optimal CPU performance.      Parameters     ----------     nu, # NOTE: The constant_folding pass is disabled in homodyne/__init__.py (+5 more)

### Community 257 - "Plot Dispatch.Py /  Handle Plotting()"
Cohesion: 0.14
Nodes (8): Test edge cases for CombinedModel., Static mode should only use diffusion parameters., Laminar flow mode should use all 7 parameters., g2 should be bounded within physical range [0.5, 2.5]., compute_g2 should require explicit dt parameter., g2 should be stable with extreme contrast values., g2 should be stable with extreme offset values., TestCombinedModelEdgeCases

### Community 258 - "Config.Py / From Dict()"
Cohesion: 0.14
Nodes (8): Test edge cases for PhysicsConstants., EPS should be small enough to avoid division by zero but not cause underflow., MAX_EXP_ARG should prevent overflow in exp()., MIN_POSITIVE should be near machine precision limits., Q range should span typical XPCS experiments., Time range should span typical XPCS measurements., Alpha and beta bounds should be symmetric around zero., TestPhysicsConstantsEdgeCases

### Community 259 - "Testlhsgeneration / Generate Lhs Starts("
Cohesion: 0.19
Nodes (9): clip_parameters(), Clip parameters to stay within bounds.      Args:         params: Parameter arra, Test edge cases for parameter clipping., Clipping parameters already in bounds should not change them., Parameters below lower bounds should clip to lower bounds., Parameters above upper bounds should clip to upper bounds., Clipping should handle extreme values correctly., Mismatched parameter count should raise ValueError. (+1 more)

### Community 260 - ".Test Compute C2 Shape() / .Test Compute"
Cohesion: 0.16
Nodes (8): Test HDF5 format detection functionality., Create mock APS old format HDF5 file., Create mock APS-U new format HDF5 file., Test detection of APS old format., Test detection of APS-U new format., Test format detection error handling., Test format detection with empty HDF5 file., TestHDF5FormatDetection

### Community 261 - ".  Str  () / .To Dict()"
Cohesion: 0.19
Nodes (10): clear_meshgrid_cache(), Clear the meshgrid cache.      Call this when switching between datasets or when, Reset cache statistics counters.      Performance Optimization (Spec 006 - FR-01, reset_cache_stats(), Tests for meshgrid cache with 23-angle dataset support (T040)., T040: Verify meshgrid cache can hold 23 unique angles., T010: Verify LRU eviction evicts least recently used entry.          Performance, T011: Verify cache hit rate > 80% for 23-angle multi-start.          Performance (+2 more)

### Community 262 - "Testjaxcompilationexpanded / .Test Jit F"
Cohesion: 0.14
Nodes (8): Expanded JIT compilation tests per TEST_REGENERATION_PLAN.md.      Tests: JIT co, Test that JIT compilation caches on first call., Test that shape changes trigger recompilation., Test that JIT compilation preserves numerical accuracy., Test JIT with static arguments using functools.partial., Test JIT compilation of g1_diffusion function., Test nested JIT compilation works correctly., TestJAXCompilationExpanded

### Community 263 - "Testmeshgridcache / Reset Cache Stats()"
Cohesion: 0.19
Nodes (9): Validate parameter names against expected names for analysis mode.      Paramete, validate_parameter_names(), Test parameter name validation functions., Validate correct static parameter names., Validate correct laminar flow parameter names., Test validation fails with wrong order (strict mode)., Test validation fails with missing parameters., Test validation fails with extra parameters. (+1 more)

### Community 264 - ".Test Success False Failed() / Determine"
Cohesion: 0.14
Nodes (8): Test parameter bounds functionality., Test getting bounds for laminar flow mode., Test getting bounds for static mode., Test getting bounds for all parameters., Test bounds override from configuration., Test getting bounds as tuple format., Test getting bounds as numpy arrays., TestParameterBounds

### Community 265 - "Result Saving.Py / Save Mcmc Results()"
Cohesion: 0.19
Nodes (9): calculate_adaptive_chunk_size(), Calculate optimal chunk size based on available system memory and parameter coun, Tests for calculate_adaptive_chunk_size() function., Chunk size should not go below minimum., Chunk size should not exceed maximum., More memory should allow larger chunks., More parameters should result in smaller chunks., Zero angles should still return valid chunk size. (+1 more)

### Community 266 - ".As Dict() /  Json Safe()"
Cohesion: 0.14
Nodes (8): Phase logs start and completion with duration., PhaseContext has correct duration after exit., Memory tracking populates memory_peak_gb., Operations faster than threshold don't log completion., Custom logger is used when provided., PhaseContext has all expected attributes., T007: Tests for log_phase() context manager., TestLogPhase

### Community 267 - ".Test Batch Statistics Export() / .Test "
Cohesion: 0.15
Nodes (10): from_dict(), from_yaml(), HybridRecoveryConfig, NLSQ configuration dataclass and validation.  This module provides the NLSQConfi, Configuration for hybrid streaming optimizer recovery strategy.      T029: Imple, Check if configuration is valid.          Returns         -------         bool, Get settings for a specific retry attempt.          Parameters         ---------, # NOTE: Subsampling is explicitly NOT supported per project requirements. (+2 more)

### Community 268 - "Config Factory.Py / Create Empty Ranges "
Cohesion: 0.16
Nodes (9): Tests for ResultValidator class., Valid result passes all validation., Invalid covariance triggers warning., Strict mode raises on failure., TestResultValidator, Validator for NLSQ optimization results.      Validates optimized parameters, co, Initialize ResultValidator.          Parameters         ----------         stric, Validate all result components.          Parameters         ----------         p (+1 more)

### Community 269 - ".Stop() / .Start()"
Cohesion: 0.2
Nodes (8): Tests for validate_optimized_params function., Finite parameters pass., Parameters within bounds pass., Parameters outside bounds fail., Small boundary violations within tolerance pass., TestValidateOptimizedParams, Validate that optimized parameters are finite and within bounds.      Parameters, validate_optimized_params()

### Community 270 - "Teststage7Nlsqpriorsconfig / .Test Defau"
Cohesion: 0.19
Nodes (9): Tests for validate_covariance function., Valid covariance matrix passes., Wrong shape covariance fails., NaN in covariance fails., Asymmetric covariance fails., Negative diagonal element fails., TestValidateCovariance, Validate covariance matrix properties.      Parameters     ----------     covari (+1 more)

### Community 271 - "Main() / Create Parser()"
Cohesion: 0.14
Nodes (8): Test HomodyneModel C2 computation methods., Test that compute_c2 returns correct shape., Test that computed C2 values are finite., Test that C2 values are positive (with default offset=1.0)., Test single angle computation., Test that contrast parameter affects results., Test that repeated calls give identical results., TestHomodyneModelComputation

### Community 272 - "Testlogphase / .Test Custom Logger()"
Cohesion: 0.15
Nodes (8): PhysicsFactors, Validate physics factors after initialization., Validate physics factors for physical consistency.          Checks:         1. A, Convert to tuple for JIT-compatible function calls.          Returns the two pre, Convert to dictionary for serialization or inspection.          Returns, Human-readable string representation., Detailed string representation., Pre-computed physics factors for XPCS correlation calculations.      This immuta

### Community 273 - "Main() / Count Dir()"
Cohesion: 0.21
Nodes (13): _get_warmstart_reduced_chi2(), load_nlsq_result_from_file(), _log_warmstart_physical_params(), Optimization runner for Homodyne CLI.  Handles NLSQ optimization dispatch and NL, Extract reduced chi-squared from an NLSQ result (dict or object)., Log physical parameter values from an NLSQ warm-start result.      Accepts eithe, Validate NLSQ result quality for CMC warm-start.      Parameters     ----------, Resolve NLSQ warm-start for CMC from all possible sources.      Priority order: (+5 more)

### Community 274 - "Andrade Creep Law Gamma ~ T^(1/3) / Tayl"
Cohesion: 0.19
Nodes (13): _generate_and_plot_fitted_simulations(), generate_nlsq_plots(), _handle_plotting(), _plot_experimental_data(), _plot_fit_comparison(), _plot_simulated_data(), Plot dispatch for Homodyne CLI.  Handles plotting options for experimental data,, Generate validation plots of experimental data.      This is a wrapper that dele (+5 more)

### Community 275 - "Teststage3Shardsize /  Resolve Max Point"
Cohesion: 0.14
Nodes (8): Test --cmc-backend argument is parsed correctly., Test --cmc-plot-diagnostics flag is parsed correctly., Test --method argument accepts all valid choices., Test --method argument defaults to 'nlsq'., Test all CMC arguments can be used together with automatic selection., Test CMC-specific CLI argument parsing., Test --cmc-num-shards argument is parsed correctly., TestCMCArgumentParsing

### Community 276 - "Cpu.Py / Configure Cpu Hpc()"
Cohesion: 0.19
Nodes (9): determine_convergence_status(), Determine convergence status from optimization info.      Args:         info: Op, Tests for determine_convergence_status function., Test that success=True gives converged status., Test that max iterations message gives max_iter status., Test that general failure gives failed status., Test convergence inference from good quality., Test failure inference from poor quality. (+1 more)

### Community 277 - "Hit Rate() / Log Calls()"
Cohesion: 0.2
Nodes (13): _compute_theoretical_c2_from_mcmc(), _create_mcmc_analysis_dict(), _create_mcmc_diagnostics_dict(), _create_mcmc_parameters_dict(), _get_parameter_names(), Result saving for Homodyne CLI.  Handles saving NLSQ and MCMC/CMC optimization r, Create parameters dictionary with posterior statistics.      This is a wrapper t, Create analysis results dictionary for MCMC/CMC.      This is a wrapper that del (+5 more)

### Community 278 - "Memorypool / .Get Buffer()"
Cohesion: 0.15
Nodes (10): Save NPZ file with experimental/theoretical data and metadata.      This is a wr, _save_nlsq_npz_file(), Unit tests for NLSQ result saving and visualization functions.  This module test, Test NPZ file creation with solver/post-hoc surfaces., Test that all expected arrays are present in NPZ file., Test loading NPZ file and verifying array contents., Test 3-panel heatmap plot generation., Test that PNG files are created on disk. (+2 more)

### Community 279 - "Residual.Py / .Get Diagnostics()"
Cohesion: 0.14
Nodes (8): Test that functions work correctly with JAX JIT compilation., Test safe_exp is JIT-compatible., Test safe_sinc is JIT-compatible., Test calculate_diffusion_coefficient is JIT-compatible., Test calculate_shear_rate is JIT-compatible., Test create_time_integral_matrix is JIT-compatible., Test apply_diagonal_correction is JIT-compatible., TestJITCompatibility

### Community 280 - "Sample Xdata() / Parameter Utils.Py"
Cohesion: 0.14
Nodes (8): Fix 2: NLSQ-informed priors config fields., Default should enable NLSQ-informed priors., Default width factor should be 2.0 (tightened from 3.0)., Should parse NLSQ prior config from dict., Width factor < 1.0 should produce validation error., Width factor > 10.0 should produce validation error., to_dict should include NLSQ prior config., TestStage7NLSQPriorsConfig

### Community 281 - ".To Dict() / Fit Quality.Py"
Cohesion: 0.2
Nodes (13): create_parser(), _filter_config(), generate_config(), interactive_builder(), main(), Configuration Generator for Homodyne Analysis.  This module provides the homodyn, Generate configuration from template.      Parameters     ----------     mode :, Interactive configuration builder.      Returns     -------     dict         Bui (+5 more)

### Community 282 - "Testnlsqoptimizationmemory / .Test Jacob"
Cohesion: 0.14
Nodes (11): create_empty_ranges_config(), create_laminar_flow_filtering_config(), create_non_matching_ranges_config(), create_single_angle_range_config(), Test factory for creating phi_filtering configuration fixtures.  This module pro, Create config with enabled=True but empty target_ranges.      This tests the edg, Create config with ranges that don't match typical dataset angles.      Useful f, Create config that targets a very narrow range (effectively single angle). (+3 more)

### Community 283 - "Configfactory / Data Factory.Py"
Cohesion: 0.26
Nodes (13): count_dir(), count_lines(), file_counts(), generate_report(), generate_summary_table(), main(), Generate a full plain-text report of line counts per module., Update the Size Distribution table in the overview doc.      Returns True if cha (+5 more)

### Community 284 - "Test Config Generator.Py / Testfallbacky"
Cohesion: 0.2
Nodes (14): He et al. PNAS 2025 (Yielding of Colloidal Suspensions), Siegert Relation (c2 = 1 + beta*|c1|^2), Heterodyne Multi-Component: Planned Future Work, Heterodyne Scattering Theory (Multi-Component), Multi-Component c2 Formula (N components), Shear Banding (Attractive Suspensions, Heterodyne), Andrade Creep Law gamma ~ t^(1/3), Homodyne Scattering: Laminar Flow Model (+6 more)

### Community 285 - "Shearmodel (4 Params) / Physics Models A"
Cohesion: 0.15
Nodes (14): Glossary Term: JAX (high-performance numerical computing library), Glossary Term: JIT compilation (JAX XLA-based just-in-time compilation), Runtime CMC-Only CPU Architecture (NumPyro CMC, v2.4.1+), Runtime Environment Variables (JAX_ENABLE_X64, HOMODYNE_COMPLETION_CACHE_TTL), Runtime System README (shell completion, validation, v2.3.0+), Runtime Shell Completion System (completion.sh, context-aware, 5-min TTL cache), Runtime System Validator (homodyne-validate command), Troubleshooting: Data Loading Errors (XPCSDataFormatError, NaN, monotonicity) (+6 more)

### Community 286 - "Adr-005: Per-Angle Scaling Modes / Five-"
Cohesion: 0.19
Nodes (14): ADR-6: Gradient-Safe Floors (jnp.where vs jnp.maximum), ADR-7: JIT Cache via Config API (not env var), ADR-5: Per-Angle Scaling System (auto mode), ADR-2: Shadow-Copy Physics Implementation, NLSQ Fitting Architecture (nlsq-fitting-architecture.md), Architecture Overview (homodyne-architecture-overview.md), Physical Model Architecture (physical-model-architecture.md), Anti-Degeneracy Defense System (laminar_flow) (+6 more)

### Community 287 - "Troubleshooting Guide / Frequently Asked"
Cohesion: 0.17
Nodes (12): NumPyro model for XPCS C2 correlation function.  This module defines the probabi, NumPyro model with FIXED per-angle scaling (anti-degeneracy constant mode)., NumPyro model with FIXED per-angle scaling (anti-degeneracy constant mode)., NumPyro model with SAMPLED averaged per-angle scaling (auto mode).      This mod, NumPyro model with SAMPLED averaged per-angle scaling (auto mode).      This mod, NumPyro model with FIXED averaged per-angle scaling (NLSQ parity mode).      Thi, NumPyro model with FIXED averaged per-angle scaling (NLSQ parity mode).      Thi, xpcs_model_averaged() (+4 more)

### Community 288 - "Testunifiedmoduleapi / Get Available Bac"
Cohesion: 0.17
Nodes (11): Determine if parallel chunk COMPUTE is worthwhile.      Parameters     ---------, should_use_parallel_compute(), Fit using Out-of-Core Global Accumulation for massive datasets., _effective_param_count_for_ooc(), fit_with_out_of_core_accumulation(), Out-of-Core Global Accumulation strategy for NLSQ optimization.  Extracted from, # IMPORTANT: t1 and t2 must remain separate -- merging them into a single, # IMPORTANT: t1 and t2 must remain separate -- merging them into a single (+3 more)

### Community 289 - "Testbatchprocessing / .Test Batch Numpy "
Cohesion: 0.18
Nodes (8): managed_allocation(), MemoryPool, Memory pool for efficient buffer reuse., Get a buffer from the pool., Return a buffer to the pool., Get buffer from appropriate memory pool., Return buffer to memory pool., Optimize garbage collection based on current conditions.

### Community 290 - ".Test Basic Method() / Testunifiedmodule"
Cohesion: 0.17
Nodes (5): MemoryManagerError, MemoryPressureError, Advanced Memory Manager for Homodyne Performance Engine ========================, Base exception for memory manager errors., Raised when memory pressure becomes critical.

### Community 291 - "Testdiagonalcorrectionbasic / .Test Off "
Cohesion: 0.18
Nodes (10): benchmark_device_performance(), Benchmark CPU device performance for optimization planning.      Parameters, Tests for device benchmarking functions., Test that device benchmarking returns results dict., Test that benchmark results include device type., Tests for device benchmarking functions., Test that device benchmarking returns results dict., Test that benchmark results include test size. (+2 more)

### Community 292 - "Phi Filtering.Py / Filter Phi Angles()"
Cohesion: 0.15
Nodes (12): build_parameter_labels(), classify_parameter_status(), compute_consistent_per_angle_init(), compute_jacobian_stats(), Parameter Utilities for NLSQ Optimization.  Provides utility functions for param, Compute Jacobian statistics for diagnostics.      Parameters     ----------, Compute per-angle contrast/offset consistent with initial physical parameters., Build parameter labels including per-angle scaling parameters.      Parameters (+4 more)

### Community 293 - "Testdiffusionmodeledgecases / .Test Comp"
Cohesion: 0.15
Nodes (9): complete_static_result(), Tests for CMC results module., Test get_posterior_stats returns statistics., Test get_samples_array returns correct shape., Test get_samples_array preserves parameter order., Tests for CMCResult methods., result_with_samples(), sample_result() (+1 more)

### Community 294 - ".Test Sinc At Zero() / Testnumericalstab"
Cohesion: 0.19
Nodes (10): FitQualityConfig, FitQualityReport, _is_physical_param(), Fit quality validation for NLSQ results (T056).  Provides post-optimization qual, Report from fit quality validation.      Attributes     ----------     passed :, Convert to dictionary for saving in results., Check if a parameter label is for a physical parameter (not per-angle scaling)., Validate fit quality and log warnings.      Parameters     ----------     result (+2 more)

### Community 295 - "Estimate Correlation Time() / .Test Esti"
Cohesion: 0.23
Nodes (6): _apply_fallback_replacement(), Tests for config_generator YAML escaping and text-replacement fallback., All special characters combined in a single value., Reproduce the text-replacement logic from interactive_builder's fallback path., Test that the text-replacement fallback produces valid YAML with special charact, TestFallbackYamlRoundTrip

### Community 296 - "Parameter Names.Py / Verify Samples Dict"
Cohesion: 0.19
Nodes (9): Determine optimal shard size based on mode, data volume, and angle count.      N, _resolve_max_points_per_shard(), Fix 3: Increased shard sizes for laminar_flow., MIN_SHARD_SIZE_LAMINAR is 3K after reparameterization fix., 3M points, 3 angles should produce shard size >= 3K., Static mode shard sizes should still be much larger than laminar., User-specified shard size should be used (if above minimum)., TestStage3ShardSize (+1 more)

### Community 297 - "Testcrosscodingconsistency / Test Parame"
Cohesion: 0.18
Nodes (9): ConfigFactory, create_edge_case_parameters(), create_parameter_sweep(), create_realistic_parameters(), ParameterFactory, Test Data Factory for Homodyne ==================================  Factory funct, Factory for creating test configurations., Factory for creating parameter sets for testing. (+1 more)

### Community 298 - "Testconfigvalidationlogging / .Test Conf"
Cohesion: 0.28
Nodes (13): CombinedModel (3 or 7 params, primary), _compute_g1_total_with_precomputed() JIT kernel, _compute_g2_scaled_core() JIT kernel, GradientCapabilityMixin (JAX/NumPy gradient dispatch), ShardGrid Precomputation (eliminates O(N log G) per NUTS step), PhysicsFactors: wq_dt and sinc_prefactor (pre-computed per shard), DiffusionModel (3 params), Physics Models API Doc (+5 more)

### Community 299 - ".Get Parameter Bounds() / .Get Active Pa"
Cohesion: 0.18
Nodes (9): create_model(), get_available_models(), Factory function to create appropriate model for analysis mode.      Args:, Get list of available analysis modes., Test edge cases for model factory functions., Invalid analysis mode should raise ValueError., Analysis mode should be case-sensitive., get_available_models should return a list of strings. (+1 more)

### Community 300 - "Testconfigboundsloading / Test Handling "
Cohesion: 0.21
Nodes (8): estimate_correlation_time(), Estimate characteristic correlation time for diffusion process.      For normal, Test edge cases for correlation time estimation., Normal diffusion (α=0) should give τ ≈ 1/(q²D₀)., Zero diffusion coefficient should give infinite correlation time., Anomalous diffusion should give finite correlation time., Extreme q values should give reasonable correlation times., TestCorrelationTimeEstimationEdgeCases

### Community 301 - "Testparametercounts / .Test Total Count "
Cohesion: 0.17
Nodes (7): Test edge cases for DiffusionModel., g1 at zero time difference should be 1 (perfect correlation)., g1 at large time difference should decay towards 0., g1 computation should be stable with extreme α values., g1 with zero D0 but non-zero D_offset should still work., Parameter bounds should cover physically meaningful range., TestDiffusionModelEdgeCases

### Community 302 - "Testparametermanagerinit / .Test Init Wi"
Cohesion: 0.17
Nodes (10): create_anisotropic_ranges(), create_isotropic_ranges(), filter_phi_angles(), filter_phi_angles_jax(), Phi Angle Filtering Module  This module provides functionality for filtering phi, Convenience function for filtering phi angles.      This is the main entry point, Create default target ranges for anisotropic analysis.      Returns anisotropic-, Create default target ranges for isotropic analysis.      For isotropic systems, (+2 more)

### Community 303 - ".Test Summary Values() / Testcmcresulted"
Cohesion: 0.17
Nodes (8): Unit Tests for Parameter Operations ====================================  **Cons, Test parameter extraction from config ordering., Test that we correctly understand config parameter ordering., Integration tests verifying parameter names are consistent across all modules., Verify mcmc.py and pjit.py use identical static parameter names., Verify mcmc.py and pjit.py use identical laminar flow parameter names., TestCrossCodingConsistency, TestParameterExtractionFromConfig

### Community 304 - "Should Use Pool() / .Test Pool Single Wo"
Cohesion: 0.17
Nodes (9): get_parameter_description(), get_physical_param_names(), Parameter Name Constants for Homodyne Analysis =================================, Get physical parameter names only (without scaling params).      Unlike get_para, Get description for parameter.      Parameters     ----------     param_name : s, Verify samples dictionary contains all expected parameters.      This function s, verify_samples_dict(), Test verify_samples_dict with complete samples. (+1 more)

### Community 305 - ".  Init  () / Testestimatephysicalworker"
Cohesion: 0.17
Nodes (7): Test parameter counting methods., Test effective parameter count for laminar flow., Test effective parameter count for static mode., Test total parameter count for laminar flow., Test total parameter count for static mode., Test getting all parameter names including scaling., TestParameterCounts

### Community 306 - " Echo Worker() /  Error Worker()"
Cohesion: 0.17
Nodes (7): Tests for ParameterManager initialization., Test initialization without config dict., Test initialization with static mode., Test initialization with laminar_flow mode., Test initialization with config dictionary., Test that caching is enabled by default., TestParameterManagerInit

### Community 307 - "From Dict() / Is Enabled()"
Cohesion: 0.17
Nodes (7): Tests for loading bounds from configuration., Test loading bounds from config overrides defaults., Test that unspecified bounds keep default values., Test handling of missing bounds section in config., Test handling of empty config., Test that string numbers in YAML are converted to floats., TestConfigBoundsLoading

### Community 308 - ".Test Single Angle() / .Test Laminar Flo"
Cohesion: 0.18
Nodes (8): Create human-readable diagnostics summary.      Parameters     ----------     r_, summarize_diagnostics(), Test summary returns expected string format., Test summary includes correct values., Test edge cases for CMC result handling., High R-hat should indicate non-convergence., Divergences should be noted in summary., TestCMCResultEdgeCases

### Community 309 - "Testvalidatenonaninf / .Test Inf Detecte"
Cohesion: 0.17
Nodes (7): Determine if worker pool is beneficial.      Parameters     ----------     n_sha, should_use_pool(), Verify fallback to per-shard spawn for < 3 shards., Verify pool is used for >= 3 shards., Verify exact boundary condition at n_shards=3., Verify pool decision with single worker., Test that pool is not used when n_shards < 3.

### Community 310 - "Testvalidateinitialparams / None Bounds "
Cohesion: 0.17
Nodes (7): expand_per_angle_parameters(), Expand compact parameters to per-angle format.      When per_angle_scaling=True, Test parameter expansion for laminar flow mode (7 physical params)., Test that mismatched parameter count raises ValueError., Test expansion with single angle., Test parameter expansion for static mode (3 physical params)., Test parameter expansion with bounds.

### Community 311 - "Experimental Plots.Py / Plot Fit Compari"
Cohesion: 0.18
Nodes (11): create_ooc_kernels(), _ooc_compute_chi2_chunk(), _ooc_compute_chunk(), _ooc_worker_cleanup(), _ooc_worker_init(), Parallel chunk accumulation for NLSQ streaming optimizer.  Dispatches chunk comp, Create JIT-compiled OOC chunk kernels from physics constants.      This is the s, Close shared memory handles on worker exit. (+3 more)

### Community 312 - "Angle In Range() / Angle Filtering.Py"
Cohesion: 0.17
Nodes (7): T006: Tests for with_context() function., Context is formatted as [key=value] prefix., Nested calls merge contexts (inner overrides outer)., Inner context overrides outer on key conflicts., None values are filtered from context., Empty context produces no prefix., TestWithContext

### Community 313 - ".Test Estimate From Valid G2() / Testnls"
Cohesion: 0.21
Nodes (11): _plot_1d_experimental_data(), _plot_2d_experimental_data(), _plot_3d_experimental_data(), plot_experimental_data(), plot_fit_comparison(), Experimental data plotting functions for homodyne XPCS analysis.  This module pr, Plot 3D experimental data (n_phi, n_t1, n_t2)., Plot 2D experimental data (single correlation matrix). (+3 more)

### Community 314 - ".  Init  () / Streamingexecutor"
Cohesion: 0.23
Nodes (11): angle_in_range(), apply_angle_filtering(), apply_angle_filtering_for_optimization(), apply_angle_filtering_for_plot(), normalize_angle_to_symmetric_range(), Angle filtering utilities for homodyne XPCS analysis.  This module provides func, Core angle filtering logic shared by optimization and plotting.      Filters phi, Normalize angle(s) to [-180°, 180°] range.      The horizontal flow direction is (+3 more)

### Community 315 - "Testcmcargumentvalidation / .Test Valid "
Cohesion: 0.17
Nodes (7): T050: Tests for configuration validation logging., Key configuration values are logged at INFO level., Default value applications are logged at DEBUG level., Unusual but valid settings are logged with warnings., Analysis mode normalization is logged at DEBUG level., Config version mismatch triggers warning., TestConfigValidationLogging

### Community 316 - "Testcmcoptions / .Test Cmc Options Warne"
Cohesion: 0.17
Nodes (7): Test data loading API function availability., Test configuration API function availability., Test public API stability and structure., Test main package import structure., Test core API function availability., Test optimization API function availability., TestPublicAPIStability

### Community 317 - ".Test Method Mcmc Accepted() / .Test Met"
Cohesion: 0.17
Nodes (7): Tests for T092: Config validation., Test validation passes for valid config values., Test validation catches invalid loss function., Test validation catches negative max_iterations., Test validation catches negative tolerance values., Test safe_int handles various input types., TestNLSQConfigValidation

### Community 318 - "Compute Uncertainties() / Testcomputeunc"
Cohesion: 0.21
Nodes (6): Check if static analysis mode is enabled., Get or create cached ParameterManager.          This avoids creating a new Param, Get parameter bounds from configuration (cached).          Uses cached Parameter, Get list of active (physical) parameters from configuration (cached).          U, Get initial parameter values from configuration.          Loads initial paramete, Calculate mid-point default values from parameter bounds.          Returns

### Community 319 - ".Test Scalar Layout Expanded() / Testext"
Cohesion: 0.17
Nodes (7): Test that MCMC convergence quality is maintained in v2.1.0., Verify convergence diagnostics meet MCMC standards.          Expected ranges (fr, Verify parameter recovery accuracy unchanged from v2.0.          Tests that v2.1, Verify automatic NUTS/CMC selection doesn't degrade convergence.          Tests, Verify config-driven initialization helps or maintains convergence.          Tes, Verify v2.1.0 handles v2.0 config format correctly.          Tests that old conf, TestMCMCConvergenceQuality

### Community 320 - "Testextractnlsqmetadata /  Extract Nlsq "
Cohesion: 0.17
Nodes (7): Unique phi values are computed., Weights are included when provided., Weights are None when not provided., Tests for _prepare_data() method., Input arrays are converted to float64., Prepared data includes point count., TestPrepareData

### Community 321 - "Testpreparedata / Unique Phi Values Are "
Cohesion: 0.18
Nodes (8): ExecutionResult, Execute standard curve_fit optimization., Execute large dataset optimization., Execute streaming optimization using AdaptiveHybridStreamingOptimizer., Result from optimization execution.      Attributes:         popt: Optimized par, Tests for ExecutionResult dataclass., Test basic ExecutionResult instantiation., TestExecutionResult

### Community 322 - ".Test Handles None Input() / Testtransfo"
Cohesion: 0.21
Nodes (8): Streaming optimization for unlimited dataset sizes.      Uses NLSQ's AdaptiveHyb, Initialize streaming executor.          Args:             checkpoint_config: Con, StreamingExecutor, Tests for StreamingExecutor class., Test StreamingExecutor name property., Test StreamingExecutor supports progress., Test StreamingExecutor with checkpoint config., TestStreamingExecutor

### Community 323 - ".To Original() / . Smooth Bound()"
Cohesion: 0.17
Nodes (7): Tests for validate_initial_params function., Parameters within bounds pass., Parameters at exact bounds pass., Parameters below lower bound fail., Parameters above upper bound fail., None bounds always passes., TestValidateInitialParams

### Community 324 - "Testconfigwidthfactor / From Dict Uses 2"
Cohesion: 0.21
Nodes (8): Tests for validate_no_nan_inf function., Array with finite values passes., NaN values are detected., Inf values are detected., Negative Inf values are detected., TestValidateNoNanInf, Validate that array contains no NaN or Inf values (T027).      Parameters     --, validate_no_nan_inf()

### Community 325 - "Testcvdispatchedgecases / .Test Cv With "
Cohesion: 0.17
Nodes (7): Unit tests for homodyne.utils.path_validation module.  Tests path validation uti, Integration tests for path validation., Test that validated paths can be written to., Test complete plot save path validation flow., Test various security edge cases., Test Windows-style path separators are handled., TestPathValidationIntegration

### Community 326 - "Teststage6Effectivemodewithwarmstart / ."
Cohesion: 0.17
Nodes (9): get_available_backends(), get_diagonal_correction_methods(), Return list of available correction methods., Return list of available backends., Tests for the unified diagonal_correction module API (v2.14.2+)., Test backend discovery function., Test method discovery function., Test backward compatibility via jax_backend re-export. (+1 more)

### Community 327 - "Teststage7Nlsqpriorbuild / Build Nlsq In"
Cohesion: 0.21
Nodes (8): apply_diagonal_correction_batch(), Apply diagonal correction to a batch of correlation matrices.      Efficiently p, Tests for batch processing functionality (v2.14.2+)., Test batch processing with NumPy backend., Test that batch results are equivalent across backends., Test batch processing with statistical method., Test batch processing with realistic XPCS data sizes., TestBatchProcessing

### Community 328 - "Test Config.Py / Testreparameterizationc"
Cohesion: 0.17
Nodes (7): Test that diagonal values are interpolated from off-diagonal neighbors, Test output shape matches input shape, Test output dtype matches input dtype, Test that off-diagonal elements remain exactly unchanged, Test suite for basic diagonal correction functionality, Test basic functionality with simple 3x3 matrix, TestDiagonalCorrectionBasic

### Community 329 - "Testparamawareshardsizing / .Test Scales"
Cohesion: 0.17
Nodes (7): Tests for different correction methods in unified module., Test basic diagonal correction method., Test statistical method with median estimator., Test statistical method with mean estimator., Test interpolation method with linear interpolation., Test that different methods handle outliers differently., TestUnifiedModuleMethods

### Community 330 - "Test Cli Commands.Py / Testconfiggenerat"
Cohesion: 0.17
Nodes (7): Test that accepted methods (nlsq, mcmc) work correctly., Test that --method nlsq is accepted., Test that --method cmc is accepted., Test that default method is nlsq when not specified., Test that nlsq method passes validation., Test that mcmc method passes validation., TestAcceptedMethodsFunctionality

### Community 331 - "Validation.Py / Validate Plot Arrays()"
Cohesion: 0.17
Nodes (7): Test validation of CMC-specific CLI arguments., Test negative --cmc-num-shards is rejected., Test zero --cmc-num-shards is rejected., Test positive --cmc-num-shards is accepted., Test invalid --cmc-backend choice is rejected by argparse., Test all valid backend choices are accepted., TestCMCArgumentValidation

### Community 332 - "Testpublicapistability / .Test Core Api "
Cohesion: 0.21
Nodes (8): _extract_nlsq_metadata(), Extract required metadata for NLSQ theoretical fit computation.      Implements, Test conversion of 2D meshgrid time arrays to 1D arrays., Test metadata extraction with multi-level fallback., Test metadata extraction when all fields are present in config., Test L extraction with fallback to sample_detector_distance., Test behavior when q is missing from data., TestExtractNLSQMetadata

### Community 333 - "Static Plotting Config Section / Glossar"
Cohesion: 0.21
Nodes (8): extract_parameters_from_result(), Extract contrast, offset, and physical parameters from result.      Handles both, Test parameter extraction with per-angle layout for laminar flow., Test that scalar layout is expanded with warning., Test that invalid parameter count raises ValueError., Tests for extract_parameters_from_result function., Test parameter extraction with per-angle layout for static mode., TestExtractParametersFromResult

### Community 334 - ".Cleanup() / .  Init  ()"
Cohesion: 0.17
Nodes (7): Test numerical stability of physics utility functions., Test safe_exp handles extreme values without overflow., Test diffusion coefficient with extreme alpha values., Test shear rate with extreme beta values., Test time integral matrix with large input values., Test time integral matrix with small input values., TestNumericalStability

### Community 335 - "Out Of Core.Py /  Effective Param Count "
Cohesion: 0.21
Nodes (8): Transform initial values from original to normalized space.      Parameters, transform_initial_values_to_z(), Tests for transform_initial_values_to_z function., Test that values are correctly transformed to z-space and back., Test that output keys have _z suffix., Test that None input returns empty dict., Test that missing parameters are skipped., TestTransformInitialValuesToZ

### Community 336 - "Main() / Run Benchmark()"
Cohesion: 0.18
Nodes (8): Transform from normalized to original space with smooth bounding., Transform samples from normalized to original space.      Parameters     -------, Smoothly bound a value to (low, high) using tanh.          Maps ℝ → (low, high), transform_samples_from_z(), Tests for transform_samples_from_z function., Test that z-space samples are correctly transformed., Test that transformed samples stay within bounds., TestTransformSamplesFromZ

### Community 337 - "Testmoduleexports / Test Device Detectio"
Cohesion: 0.2
Nodes (9): build_nlsq_informed_prior(), build_nlsq_informed_priors(), Build a TruncatedNormal prior centered on NLSQ estimate.      This provides info, Build informative priors for all physical parameters from NLSQ results.      Par, Fix 2: verify build_nlsq_informed_prior produces correct distribution., Prior should be centered on NLSQ estimate., Prior scale should be nlsq_std * width_factor., Without NLSQ std, prior should use 10% of range. (+1 more)

### Community 338 - "  Init  () / .Start Monitoring()"
Cohesion: 0.21
Nodes (8): estimate_contrast_offset_from_data(), Estimate contrast and offset from C2 data using physics-informed quantile analys, Verify offset is estimated from large-lag region., Tests for estimate_contrast_offset_from_data function., Verify estimation recovers known contrast/offset within tolerance., Verify estimates are clipped to valid bounds., Verify fallback to midpoint with insufficient data., TestEstimateContrastOffsetFromData

### Community 339 - ".  Init  () / From Config()"
Cohesion: 0.21
Nodes (8): get_init_value(), Get initial value for a parameter.      Priority:     1. Value from initial_valu, Tests for get_init_value function., Test getting value from initial_values dict., Test falling back to midpoint when no initial value., Test falling back when parameter not in initial_values., Test midpoint calculation for contrast., TestGetInitValue

### Community 340 - ".Get() / Cpuprofiler"
Cohesion: 0.17
Nodes (11): _counting_worker(), _echo_worker(), _error_worker(), _init_fn_that_sets_flag(), Tests for persistent CMC worker pool., Worker that reports its PID to verify reuse., Worker that raises on request., Worker that puts results on an external queue and returns None. (+3 more)

### Community 341 - "Scalings() / Test Scaling.Py"
Cohesion: 0.2
Nodes (8): Initialize multiprocessing backend.          Parameters         ----------, _estimate_physical_workers(), Estimate the number of worker processes from physical core count.      Uses :fun, Test _estimate_physical_workers helper., Physical core detection reserves 1 core for the main process., Single-core system still guarantees at least 1 worker., Falls back to os.cpu_count() when detect_cpu_info is unavailable., TestEstimatePhysicalWorkers

### Community 342 - "Demo Forced Cmc() / Demo Forced Nuts()"
Cohesion: 0.21
Nodes (8): load_samples_npz(), Load samples from npz file.      Parameters     ----------     input_path : Path, Tests for load_samples_npz function., Test loading nonexistent file raises FileNotFoundError., Test loading non-npz file raises ValueError., Test loading directory raises ValueError., Test path with .. is resolved., TestLoadSamplesNpz

### Community 343 - "Docs Index / Api: Core Module"
Cohesion: 0.17
Nodes (7): P3: CV dispatch edge cases — parameter_space=None, invalid bounds., parameter_space=None falls back to mean-based scale (inflated CV)., param_range == 0 (lo == hi) falls back to mean-based scale., lo > hi → negative param_range → uses abs(range) for scale., Inverted bounds should use abs(range) for near-zero params, not fall back., Near-zero param with valid bounds → small CV (suppressed false positive)., TestCVDispatchEdgeCases

### Community 344 - "Test Suite Readme (V2.4.1, 47 Unit Files"
Cohesion: 0.17
Nodes (7): Fix 1: Default to constant_averaged when NLSQ warm-start present., auto + NLSQ warm-start should upgrade to constant_averaged., auto without warm-start should stay as auto., auto with no nlsq_per_angle_mode should auto-select normally., Explicit individual mode should not be overridden by warm-start., NLSQ constant mode should be preserved even with warm-start., TestStage6EffectiveModeWithWarmstart

### Community 345 - "Nlsq Fit Quality Plot / Cmc Posterior Pl"
Cohesion: 0.17
Nodes (7): Unit tests for CLI command-line interface.  Tests for config generator, argument, Tests for default argument values., Test that mode defaults to None., Test that output defaults to None., Test that all boolean flags default to False., Test that validate defaults to None., TestConfigGeneratorDefaults

### Community 346 - "Numerical Correctness Tests / Testdiagon"
Cohesion: 0.17
Nodes (7): Test that integer arrays are considered clean., Test that zero values are considered valid., Test with more names than arrays., Test that empty arrays are considered clean., Pre-plot data validation utilities.  Lightweight checks for NaN/Inf in arrays be, Check arrays for NaN/Inf values before plotting.      Parameters     ----------, validate_plot_arrays()

### Community 347 - "Time Array Should Start From 0. / Testti"
Cohesion: 0.18
Nodes (3): from_config(), from_dict(), Anti-Degeneracy Controller - Orchestrator for 5-Layer Defense System.  This modu

### Community 348 - "Testvalidationcomponentedgecases / .Test"
Cohesion: 0.17
Nodes (7): FallbackInfo, FunctionEvaluationCounter, NLSQ optimization result classes.  This module extracts result dataclasses from, Tracks fallback from NLSQAdapter to NLSQWrapper.      Included in OptimizationRe, Convert to dict for inclusion in device_info., Wraps a callable and counts invocations.      Useful for tracking the number of, Call the wrapped function and increment count.

### Community 349 - "Testshearmodeledgecases / .Test Sinc Squ"
Cohesion: 0.21
Nodes (12): ADR-001: JAX CPU-Only Backend, JAX_ENABLE_X64 Float64 Configuration, Synchrotron Beamline Deployment Environment, ADR-003: Anti-Degeneracy Defense System, ADR-004: Consensus Monte Carlo for Bayesian Inference, max_points_per_shard Auto Configuration, Shard-Posterior Partitioning Strategy, ADR-005: Per-Angle Scaling Modes (+4 more)

### Community 350 - "Testgradientwithrealparameters / .Test N"
Cohesion: 0.21
Nodes (12): Appendices Index (Section 05: troubleshooting, FAQ, glossary), FAQ: Configuration Questions (template gen, validation, gap_distance units), Frequently Asked Questions Guide, FAQ: NLSQ Optimization (convergence, speed, CMA-ES), Glossary of XPCS and Homodyne Terms, Glossary Term: g1 (first-order field correlation function), Glossary Term: g2 (second-order intensity correlation function), Glossary Term: Latin Hypercube Sampling (multi-start NLSQ) (+4 more)

### Community 351 - ".Get Cmc Config() / . Merge Cmc Config()"
Cohesion: 0.21
Nodes (12): Static Analysis Mode Config (analysis_mode: static), Static NLSQ Config Section (convergence, streaming, anti-degeneracy disabled), Static Parameter Space (D0, alpha, D_offset bounds + priors), Static Plotting Config Section, Static Reparameterization Config (D_total, log-gamma disabled), YAML Template: homodyne_master_template.yaml (all options), YAML Template: homodyne_static.yaml (3-parameter diffusion), FAQ: Analysis Mode Selection (static vs laminar_flow) (+4 more)

### Community 352 - "Testintegrationscenarios / .Test Explora"
Cohesion: 0.2
Nodes (9): ADR-1: CPU-Only Architecture Decision, benchmark_cpu_performance(), configure_cpu_hpc(), _configure_jax_cpu(), detect_cpu_info(), ADR: CPU-Only Architecture (no GPU), TestCPUDetection, TestDeviceBenchmarking (+1 more)

### Community 353 - "Testmissingrequiredfields / .Test Parame"
Cohesion: 0.17
Nodes (11): ADR-3: Lazy Import System, DOI 10.1073/pnas.2401162121 (2024 paper), DOI 10.1073/pnas.2514216122 (2025 paper), Furo Sphinx Theme, Sphinx conf.py, XPCSDataLoader, Float64 Enforcement (JAX_ENABLE_X64), homodyne/__init__.py (package init) (+3 more)

### Community 354 - "Testnlsqconfigvalidation / Tests For T09"
Cohesion: 0.22
Nodes (4): OOCSharedArrays, Shared memory manager for OOC flat data arrays.      Parameters     ----------, Get picklable shared memory references., Close and unlink all shared memory blocks.

### Community 355 - "Testinitialparametersloading / .Test Val"
Cohesion: 0.25
Nodes (7): __init__(), MemoryPressureMonitor, Real-time memory pressure monitoring with adaptive responses.      Monitors syst, Start background memory pressure monitoring., Register callback for warning-level memory pressure., Register callback for critical-level memory pressure., Register callback for memory pressure recovery.

### Community 356 - "Testedgecases / .Test Zero Values()"
Cohesion: 0.2
Nodes (7): Initialize HomodyneModel from configuration dictionary.          Parameters, Extract and validate configuration parameters., Determine analysis mode from configuration., create_physics_factors_from_config_dict(), from_config(), Physics Factors Pre-computation Module ========================================, Create PhysicsFactors from a homodyne configuration dictionary.      Convenience

### Community 357 - "Testconfignormalization / .Test Normaliz"
Cohesion: 0.18
Nodes (6): Tests for CMC parameter scaling module.  This module tests the non-centered para, Tests verifying gradient balancing behavior., Test that parameter scale ratio is dramatically reduced after normalization., Test D0 uses linear scaling (ParameterScaling is always linear z-space)., scalings(), TestGradientBalancing

### Community 358 - ".Test Static Mode Parameters() / .Test L"
Cohesion: 0.18
Nodes (10): demo_automatic_selection(), demo_backward_compatibility(), demo_forced_cmc(), demo_forced_nuts(), demo_result_inspection(), Demonstrate backward compatibility (v2.1.0)., Demonstrate how to inspect results., Demonstrate automatic method selection (v2.1.0). (+2 more)

### Community 359 - "Testactiveparameters / Test Active Param"
Cohesion: 0.18
Nodes (11): Speckle Contrast beta(phi_k) Angular Dependence, Shear Integral Gamma(t1,t2) via Cumulative Trapezoid, Theory Citations and Bibliography, He et al. PNAS 2024 (Transport Coefficient Framework), Correlation Functions Theory, Cumulative Trapezoid Integration for int D(t) dt, g2(q, tau) Equilibrium Approximation, Speckle Contrast beta (Optical Coherence Parameter) (+3 more)

### Community 360 - ". Build Z Space Init() / Testreparamwarm"
Cohesion: 0.18
Nodes (11): FAQ: Results Questions (chi-squared, saving posteriors, comparing NLSQ vs CMC), Glossary Term: ArviZ (Bayesian model diagnostics and visualization), Glossary Term: C2 (two-time correlation function), Glossary Term: ESS (Effective Sample Size), Glossary Term: R-hat (Gelman-Rubin convergence statistic), C2 Two-Time Correlation Heatmap Plot, CMC Posterior Plots (ArviZ), NLSQ Fit Quality Plot (+3 more)

### Community 361 - "Jacobian.Py / Compute Jacobian Stats()"
Cohesion: 0.18
Nodes (11): Glossary Term: anomalous diffusion (MSD ~ t^α, α≠1), Test Coverage Requirements (80% min, 90% critical modules), Test Factories (6 files: data_factory, synthetic_data, config_factory, large_dataset_factory), Integration Tests (7 files: NLSQ, MCMC, CMC, parameter recovery, edge cases), Test Markers (unit, integration, performance, mcmc, property, slow, requires_jax, linux), Performance Tests (6 files: benchmarks, NLSQ speed, chunking, angle filtering), Property-Based Tests (2 files, Hypothesis: mathematical invariants), Regression Tests (2 files: NLSQ stability, save/load compatibility) (+3 more)

### Community 362 - ".  Exit  () / .Shutdown()"
Cohesion: 0.2
Nodes (11): YAML Template: homodyne_laminar_flow.yaml, Glossary Term: Couette geometry (concentric-cylinder shear cell), Glossary Term: gamma_dot_0 (reference shear rate, s⁻¹), Glossary Term: laminar_flow analysis mode (7 parameters), Glossary Term: sinc (sinc² shear-induced decorrelation term), Scripts: Benchmarks (benchmark_onednn.py), Scripts: CMC/NUTS MCMC Demos (mcmc_uncertainty.py, cmc_large_dataset.py), Scripts: NLSQ Demos (static, laminar flow, streaming, overlays, CPU tuning) (+3 more)

### Community 363 - "Stratified Ls.Py / Create Stratified Chu"
Cohesion: 0.22
Nodes (11): ADR-4: NLSQ-First Workflow, CMC Fitting Architecture (cmc-fitting-architecture.md), Bimodal Posterior Detection & Mode-Aware Consensus, CMCConfig (113 edges), Consensus Monte Carlo (CMC) Algorithm, Noise-Weighted LPT Shard Scheduling, MCMCSamples (central CMC result carrier, 96 edges), NLSQ→CMC Warm-Start Integration (+3 more)

### Community 364 - "Main() / Diagnostics.Py"
Cohesion: 0.2
Nodes (6): Test edge cases for ShearModel., g1 with zero shear rate should be 1 (sinc(0)² = 1)., g1 should vary with φ₀ (flow direction angle)., g1 should be maximal when φ = φ₀ + 90° (perpendicular to flow)., sinc²(x) should always be in [0, 1]., TestShearModelEdgeCases

### Community 365 - ".Test Empty Xdata Fails() / .Test Empty "
Cohesion: 0.2
Nodes (6): Test edge cases for XPCSDataLoader initialization., Providing both config_path and config_dict should raise ValueError., Providing neither config_path nor config_dict should raise ValueError., Missing required experimental_data params should raise XPCSConfigurationError., Missing required analyzer_parameters should raise XPCSConfigurationError., TestDataLoaderInitEdgeCases

### Community 366 - "Testmoduleexports / Test Nlsq Validation"
Cohesion: 0.2
Nodes (6): Test gradient computation using realistic parameter values from configs., Test gradient computation with ACTUAL parameters from a real config file., Test that small perturbations to real parameters produce measurable changes., Test that negative parameters (common in real configs) are handled correctly., Test that gradient computation is consistent across different parameter scales., TestGradientWithRealParameters

### Community 367 - ".Test Security Edge Cases() / .Test Vali"
Cohesion: 0.2
Nodes (6): Test active parameters functionality., Test getting active parameters for laminar flow., Test getting active parameters for static mode., Test getting active parameters from configuration., Test explicit active_parameters list in config., TestActiveParameters

### Community 368 - "Testdevicebenchmarking / Benchmark Devic"
Cohesion: 0.2
Nodes (6): Integration tests for physics validation., Test validation for static mode parameters., Test validation for laminar flow parameters., Test realistic subdiffusion scenario., Test detection of problematic parameter set., TestPhysicsValidationIntegration

### Community 369 - ".  Init  () / Memorystats"
Cohesion: 0.22
Nodes (9): analyze_parameter_sensitivity(), compute_jacobian_condition_number(), compute_jacobian_stats(), estimate_gradient_noise(), Jacobian computation utilities for NLSQ optimization.  This module extracts Jaco, Analyze parameter sensitivity from Jacobian column norms.      Higher column nor, Estimate gradient noise from multiple Jacobian computations.      Computes Jacob, Compute Jacobian statistics for convergence diagnostics.      Computes the Jacob (+1 more)

### Community 370 - ".  Init  () / Parameterspace"
Cohesion: 0.22
Nodes (7): Convert stratified flat arrays into chunks for StratifiedResidualFunction., Fit using NLSQ's least_squares() with stratified residual function., create_stratified_chunks(), fit_with_stratified_least_squares(), Stratified least-squares strategy for NLSQ optimization.  Extracted from wrapper, Fit using NLSQ's least_squares() with stratified residual function.      This me, Convert stratified flat arrays into chunks for StratifiedResidualFunction.

### Community 371 - "Testrandomgeneration / Generate Random S"
Cohesion: 0.22
Nodes (7): main(), Unit tests for diagonal overlay diagnostics., test_solver_overlay_has_lower_rmse_than_posthoc(), compute_diagonal_overlay_stats(), DiagonalOverlayResult, Diagnostic helpers for visual validation of fitted C₂ surfaces., Return diagonal traces and simple statistics for a single angle.

### Community 372 - "Testhandlenlsqresult / .Test Invalid Tup"
Cohesion: 0.22
Nodes (5): OOCComputePool, Persistent process pool for parallel OOC chunk computation.      Workers share f, Dispatch all chunks to workers and collect (JtJ, Jtr, chi2) tuples.          Par, Dispatch chi2-only computation across workers (no Jacobian).          Parameters, Shut down the pool. Idempotent.

### Community 373 - "Largedatasetexecutor / Testlargedatasete"
Cohesion: 0.2
Nodes (6): MemoryStats, Comprehensive memory statistics and monitoring., Update system memory statistics., Initialize memory pressure monitor.          Args:             warning_threshold, Main monitoring loop., Update memory statistics.

### Community 374 - ".Test Shear Rate Alias() / .Test Trapezo"
Cohesion: 0.24
Nodes (6): ParameterSpace, Get parameter bounds based on analysis mode with configuration override support., Get default bound for a specific parameter name., Get parameter priors based on analysis mode., Initialize unified homodyne engine.          Args:             analysis_mode: "s, Parameter space definition with bounds and priors.      Implements specified par

### Community 375 - "Physics Utils.Py / Testcalculateshearrat"
Cohesion: 0.2
Nodes (6): Test suite for configuration schema normalization., Test that legacy data_folder_path + data_file_name is normalized to file_path., Test that modern file_path format is not modified., Test that phi angles paths are also normalized., Test normalization with absolute paths., TestConfigNormalization

### Community 376 - "Testdeprecatedmethodrejection / .Test Me"
Cohesion: 0.2
Nodes (6): Test realistic integration scenarios., Test loading NLSQ results as initial values for MCMC., Test partial optimization (fixing some parameters)., Test exploration mode using mid-point defaults., Test realistic laminar flow config with all features., TestIntegrationScenarios

### Community 377 - "Testprepareparameterdata /  Prepare Para"
Cohesion: 0.2
Nodes (6): Test edge cases and boundary conditions., Test with single parameter., Test that negative values are handled correctly., Test that very large values are handled correctly., Test that zero values are handled correctly., TestEdgeCases

### Community 378 - "Testgetphysicalparamcount / Get Physical"
Cohesion: 0.2
Nodes (6): Test with completely empty config., Test handling of malformed configuration files., Test config without analysis_mode section., Test config without initial_parameters section entirely., Test config without parameter_space section., TestMalformedConfigFiles

### Community 379 - "Testbuildresult / Tests For  Build Resul"
Cohesion: 0.2
Nodes (6): Test handling of missing required fields in config., Test initial_parameters without parameter_names., Test initial_parameters without values., Test when parameter_names and values have different lengths., Test parameter_space without bounds section., TestMissingRequiredFields

### Community 380 - ".  Repr  () / .Get Statistics()"
Cohesion: 0.24
Nodes (10): get_completion_source_path(), install_bash_completion(), install_fish_completion(), install_shell_completion(), install_zsh_completion(), Get the path to the completion script in the package.      Returns:         Path, Install bash completion script.      Args:         venv_path: Path to virtual en, Install zsh completion script.      Args:         venv_path: Path to virtual env (+2 more)

### Community 381 - "Test Residual Function.Py / Testresidual"
Cohesion: 0.2
Nodes (6): Tests for _build_result() method., Result contains all required keys., Uncertainties are computed from covariance diagonal., None covariance results in None uncertainties., Diagnostics are included when provided., TestBuildResult

### Community 382 - "Testnlsqwrappererrorhandling / .Test Err"
Cohesion: 0.2
Nodes (6): Test suite for _handle_nlsq_result() method., Test that empty tuple raises TypeError., Test that unrecognized type raises TypeError., Test that pcov dimensions match popt length., Test identity matrix created with correct size when pcov missing., TestHandleNLSQResult

### Community 383 - "Mock Config() / Mock Xpcs Data()"
Cohesion: 0.27
Nodes (7): LargeDatasetExecutor, Large dataset optimization using curve_fit_large.      Uses NLSQ's memory-effici, Tests for LargeDatasetExecutor class., Test LargeDatasetExecutor name property., Test LargeDatasetExecutor supports progress., Test LargeDatasetExecutor execution., TestLargeDatasetExecutor

### Community 384 - ".  Init  () / .Get Prior()"
Cohesion: 0.27
Nodes (6): Tests for validate_array_dimensions function., Matching array lengths pass., Different array lengths fail., TestValidateArrayDimensions, Validate that xdata and ydata have compatible dimensions.      Parameters     --, validate_array_dimensions()

### Community 385 - "Testpriortemperingscale / .Test Prior Sc"
Cohesion: 0.22
Nodes (7): Test PathValidationError exception class., Test that PathValidationError inherits from ValueError., Test that exception can be raised and caught., TestPathValidationError, PathValidationError, Path validation utilities for secure file operations.  This module provides path, Raised when path validation fails due to security concerns.

### Community 386 - "Testpriortemperingconfig / .Test Config "
Cohesion: 0.2
Nodes (6): Numerical correctness tests, Test against reference NumPy implementation from xpcs_loader.py, Test exact diagonal interpolation formula, Test that symmetric matrices remain symmetric after correction, Test that correlation structure is preserved in off-diagonal, TestDiagonalCorrectionCorrectness

### Community 387 - "Testyamlescapestring /  Yaml Escape Stri"
Cohesion: 0.2
Nodes (6): Test that deprecated methods are properly rejected with clear errors., Test that --method nuts is rejected with proper exit code., Test that --method mcmc is rejected with proper exit code (use cmc instead)., Test that --method auto is rejected with proper exit code., Test that method argument only includes nlsq and cmc., TestDeprecatedMethodRejection

### Community 388 - "Syntheticxpcsdata / Synthetic Data.Py"
Cohesion: 0.24
Nodes (7): _prepare_parameter_data(), Prepare parameter data dictionary for JSON saving.      Extracts parameter value, Test parameter data preparation for JSON saving., Test parameter extraction for static mode mode (5 params)., Test parameter extraction for laminar flow mode (9 params)., Test parameter extraction when uncertainties are None., TestPrepareParameterData

### Community 389 - "Testmcmcmoduleavailability / .Test Cmc M"
Cohesion: 0.24
Nodes (7): get_physical_param_count(), Get number of physical parameters for analysis mode.      Args:         analysis, Tests for get_physical_param_count function., Test that static mode returns 3 physical parameters., Test that laminar flow mode returns 7 physical parameters., Test that unknown mode raises ValueError., TestGetPhysicalParamCount

### Community 390 - "Testversioncompatibility / .Test Version"
Cohesion: 0.22
Nodes (7): calculate_shear_rate_cmc(), Shared Physics Utility Functions for Homodyne ==================================, Calculate time-dependent shear rate for CMC (element-wise) computations.      Th, Test suite for calculate_shear_rate_cmc function., Test CMC variant handles consecutive zeros (dt=0 case)., Test CMC variant gives similar results to regular for normal input., TestCalculateShearRateCmc

### Community 391 - "Testmcmccompatibility / Testsaveresultss"
Cohesion: 0.2
Nodes (6): Test backward compatibility aliases., Test _calculate_diffusion_coefficient_impl_jax alias exists., Test _calculate_shear_rate_impl_jax alias exists., Test _create_time_integral_matrix_impl_jax alias exists., Test _trapezoid_cumsum alias exists., TestBackwardCompatibilityAliases

### Community 392 - "Main() / Compute C2 Cmc()"
Cohesion: 0.2
Nodes (6): Tests for error handling in NLSQWrapper., TC-ERROR-001: Error recovery actions are logged., TC-ERROR-002: Max retry count is respected., TC-ERROR-003: Failure provides informative error message., TC-ERROR-004: Partial results preserved on failure., TestNLSQWrapperErrorHandling

### Community 393 - "Main() / Run Nlsq Fit()"
Cohesion: 0.2
Nodes (9): mock_config(), mock_xpcs_data(), per_angle_bounds(), per_angle_initial_params(), Unit Tests for NLSQWrapper Class ================================  Tests for hom, Create mock configuration for NLSQWrapper.fit()., Create mock XPCS data for testing., Initial parameters in v2.4.0 per-angle format. (+1 more)

### Community 394 - "Correlation Functions Theory / Theoretic"
Cohesion: 0.2
Nodes (6): Test prior_tempering config option., prior_tempering defaults to True., prior_tempering parsed from config dict., prior_tempering can be disabled., prior_tempering survives to_dict/from_dict roundtrip., TestPriorTemperingConfig

### Community 395 - "Configmanager Class / Batch Processing G"
Cohesion: 0.2
Nodes (6): num_shards=1 → prior_scale=1.0 (no tempering, backward-compatible)., Realistic test: K=150 shards (C020 dataset)., Test that prior_scale correctly widens z-space priors., Default prior_scale=1.0 gives Normal(0, 1)., With K=100 shards, prior_scale=sqrt(100)=10., TestPriorTemperingScale

### Community 396 - "Scripts And Demos Readme / Scripts: Benc"
Cohesion: 0.24
Nodes (6): MockParameterSpace, MockPriorSpec, Tests for CMC prior tempering (Scott et al. 2016).  Verifies that prior^(1/K) is, Mock PriorDistribution-like object., Mock ParameterSpace for testing without full config system., simple_parameter_space()

### Community 397 - "  Init  .Py /   Getattr  ()"
Cohesion: 0.24
Nodes (9): build_prior(), build_prior_from_spec(), extract_nlsq_values_for_cmc(), _get_base_param_name(), Prior distribution builders for CMC analysis.  This module provides utilities fo, Build NumPyro distribution from PriorDistribution specification.      Parameters, Get base parameter name for per-angle parameters.      Maps indexed scaling name, Build NumPyro prior distribution for a parameter.      Parameters     ---------- (+1 more)

### Community 398 - "Config.Py / .Is Valid()"
Cohesion: 0.27
Nodes (9): I/O utilities for CMC results.  This module provides functions for saving CMC re, Save fitted data in NLSQ-compatible format.      Parameters     ----------     r, Save posterior parameter statistics to JSON.      Parameters     ----------, Save convergence diagnostics to JSON.      Parameters     ----------     result, Save all CMC result files.      Parameters     ----------     result : CMCResult, save_all_results(), save_diagnostics_json(), save_fitted_data_npz() (+1 more)

### Community 399 - ".  Init  () / .Get Prior()"
Cohesion: 0.31
Nodes (4): Escape a string for safe insertion into YAML double-quoted values., _yaml_escape_string(), Test the YAML double-quote escape helper., TestYamlEscapeString

### Community 400 - "Adapter() / Testinheritance"
Cohesion: 0.24
Nodes (9): generate_laminar_flow_dataset(), generate_synthetic_xpcs_data(), get_per_angle_param_names(), Synthetic XPCS Data Generator for Scientific Validation (T034).  Generates synth, Generate synthetic XPCS data with known ground-truth parameters.      Uses homod, Container for synthetic XPCS data with known ground truth.      Attributes:, Generate laminar flow synthetic dataset with default parameters.      Generates, Get parameter names in correct NumPyro order for per-angle scaling.      NumPyro (+1 more)

### Community 401 - "Mock Parameter Space() / Testscalingutil"
Cohesion: 0.2
Nodes (6): MCMC Statistical Validation Tests =================================  Basic valid, Test MCMC/CMC module availability and imports., Test MCMC module availability and basic imports., Test CMC (Consensus Monte Carlo) module availability., Test NumPyro availability for MCMC sampling., TestMCMCModuleAvailability

### Community 402 - "Main() / Run Benchmark()"
Cohesion: 0.2
Nodes (7): Regression tests for _save_results() backward compatibility.  This module ensure, Test that MCMC saving is unaffected by NLSQ additions., Verify MCMC result saving functionality is unchanged., Test _save_results() signature and call site updates., Verify _save_results() accepts data and config parameters., TestMCMCCompatibility, TestSaveResultsSignature

### Community 403 - "Cmc Prior Tempering / Gradient-Safe Floo"
Cohesion: 0.2
Nodes (6): Unit tests for residual function creation in NLSQ wrapper.  Tests cover: - Resid, Test graceful error handling for missing data attributes., Test residual function creation (T012)., Verify residual function is JAX JIT-compilable.          Required for NLSQ optim, Verify residual function works with laminar flow analysis mode.          Laminar, TestResidualFunctionCreation

### Community 404 - "Viz/Nlsq Plots.Py / Viz/Mcmc Dashboard.P"
Cohesion: 0.2
Nodes (5): Calculate success rate from recent batches in buffer.          Returns         -, Calculate average loss from recent successful batches.          Returns, Calculate average iterations from recent batches.          Returns         -----, Return comprehensive statistics dictionary.          Returns         -------, Return string representation of statistics.

### Community 405 - "Ess And Bfmi Mcmc Diagnostics / Nuts (No"
Cohesion: 0.29
Nodes (9): compare_integration_methods(), compute_c2_cmc(), compute_c2_nlsq(), create_time_grid(), main(), Compare integration methods for diffusion integral.      For integral from t=0 t, Create uniform time grid., Compute C2 using NLSQ physics (meshgrid mode).      Returns C2 heatmap with shap (+1 more)

### Community 406 - "Nlsq Warm-Start For Cmc / Adr-001: Jax C"
Cohesion: 0.29
Nodes (9): create_model_function(), generate_deterministic_data(), main(), print_results(), Create model function for curve_fit.      Uses a simple exponential decay model, Run NLSQ fitting and return results., Print formatted results., Generate deterministic synthetic data using simplified model.      Uses the same (+1 more)

### Community 407 - "Glossary Term: Nuts (No-U-Turn Sampler) "
Cohesion: 0.2
Nodes (10): Five-Layer Anti-Degeneracy Defense, Gradient Collapse Monitoring (Layer 4), Hierarchical Two-Stage Optimization (Layer 2), Shear-Sensitivity Weighting at phi=0 (Layer 5), Analysis Modes (static, laminar_flow), Laminar Flow Mode (7 physical parameters), Laminar Flow Parameters: D0, alpha, D_offset, gamma_dot_t0, beta, gamma_dot_t_offset, phi0, Parameter Bounds for NLSQ and CMC Priors (+2 more)

### Community 408 - "Troubleshooting: Shell Completion Issues"
Cohesion: 0.27
Nodes (10): ADR-002: NLSQ/CMC Architectural Split, NLSQ Warm-Start for CMC, Adaptive Sampling (warmup/samples scaled by shard size), Consensus Monte Carlo (CMC) Algorithm, Computational Methods (NLSQ + CMC/NUTS), ESS and BFMI MCMC Diagnostics, Log-Space Reparameterization for NUTS Priors, Non-Linear Least Squares (NLSQ) Method (+2 more)

### Community 409 - "Main() / Get Xla Mode Path()"
Cohesion: 0.22
Nodes (10): Batch Processing Guide, HPC SLURM Job Array Processing, Multi q-Value Batch Iteration, Result Aggregation Pattern, Sequential Batch Script (batch_nlsq.py), ConfigManager Class, YAML Data Section (file_path, q_value, gap_distance, dt), YAML Optimization Section (nlsq, cmc settings) (+2 more)

### Community 410 - "Install Xla Activation() / Get Xla Confi"
Cohesion: 0.22
Nodes (8): _check_installation(), get_package_info(), __getattr__(), Homodyne: JAX-First XPCS Analysis Package ======================================, # IMPORTANT: Don't set JAX_PLATFORMS - let JAX auto-detect available backend, Lazy-load public API symbols and HAS_* flags on first access., Get comprehensive package information and status.      Returns     -------     d, Check installation status and provide helpful messages (CPU-only in v2.3.0).

### Community 411 - "Testunifiedmodulebackends / .Test Numpy "
Cohesion: 0.22
Nodes (6): from_dict(), CMC configuration dataclass and validation.  This module provides the CMCConfig, # NOTE: Defaults are intentionally conservative for laminar_flow, # NOTE: Map to multiprocessing, NOT pjit, because pjit backend is sequential, Validate configuration values.          Returns         -------         list[str, Check if configuration is valid.          Returns         -------         bool

### Community 412 - "Testjaxbackendedgecases / .Test Jit Comp"
Cohesion: 0.22
Nodes (5): Unit Tests for NLSQAdapterBase Abstract Base Class =============================, Tests that NLSQAdapter and NLSQWrapper inherit from NLSQAdapterBase., NLSQAdapter inherits from NLSQAdapterBase., NLSQWrapper inherits from NLSQAdapterBase., TestInheritance

### Community 413 - "Testparameterinfoedgecases / .Test Get P"
Cohesion: 0.22
Nodes (7): benchmark_cpu_performance(), Benchmark CPU performance for optimization planning.      Parameters     -------, Benchmark CPU performance for optimization planning.      Parameters     -------, Test that benchmark_cpu_performance returns benchmark results., Test CPU benchmark with small test size., Test that benchmark_cpu_performance returns benchmark results., Test CPU benchmark with small test size.

### Community 414 - "Testgradientsanitycheck / .Test Gradient"
Cohesion: 0.22
Nodes (5): Tests for data-driven quantile estimation of contrast/offset.  These tests verif, Tests for estimate_per_angle_scaling function., Verify per-angle estimation with different parameters per angle., Verify fallback when angle has too few data points., TestEstimatePerAngleScaling

### Community 415 - "Testregressionprevention / .Test No Phi "
Cohesion: 0.22
Nodes (5): Tests for CMC prior builders module., Test building prior for contrast parameter., Test building prior for D0 parameter., Tests for build_prior function., TestBuildPrior

### Community 416 - "Testfullmcmcworkflow / .Test Config Driv"
Cohesion: 0.25
Nodes (7): NumPyro model with reference-time reparameterized sampling space.      This mode, NumPyro model with reference-time reparameterized sampling space.      This mode, xpcs_model_reparameterized(), Tests for xpcs_model_reparameterized., Reparameterized model samples log_D_ref instead of D0., D0, D_offset, gamma_dot_t0 have correct values from transforms., TestReparameterizedModel

### Community 417 - "Testconfigmanageractiveparameters / .Tes"
Cohesion: 0.22
Nodes (5): Tests for CMC per-angle mode support (v2.18.0+).  This module tests the anti-deg, Tests for shared scaling utilities., Test the shared quantile estimation function., Test the per-angle scaling estimation function., TestScalingUtilsShared

### Community 418 - ".Test From Defaults Static() / Testparam"
Cohesion: 0.25
Nodes (4): _MockParameterSpace, Smoke tests for CMC timeout mitigation settings.  These tests ensure the lighter, Minimal ParameterSpace substitute for tests., test_laminar_flow_smoke_run_completes_quickly()

### Community 419 - "Testconfigmanagerparameterbounds / Test "
Cohesion: 0.31
Nodes (8): benchmark_ad_mode(), create_xpcs_residual_fn(), main(), Benchmark a single AD mode.      Parameters     ----------     mode : str, Run jacfwd vs jacrev benchmark for given dimensions.      Parameters     -------, Run full benchmark suite., Create a synthetic XPCS-like residual function.      Mimics the structure of hom, run_benchmark()

### Community 420 - "Testinfolevelviolations / .Test Very Low"
Cohesion: 0.28
Nodes (9): Consensus Monte Carlo Core, Angle-Balanced Sharding, CMC Prior Tempering, Scaled Optimization Model, NumPyro Probabilistic Models, Element-wise Physics for MCMC, Gradient-Safe Floor, Reference-Time Reparameterization (+1 more)

### Community 421 - "Testseverityfiltering / .Test Info Level"
Cohesion: 0.31
Nodes (9): viz/datashader_backend.py (high-perf render), viz/mcmc_arviz.py (ArviZ wrappers), viz/mcmc_comparison.py, viz/mcmc_dashboard.py, viz/mcmc_diagnostics.py, viz/mcmc_plots.py (re-export hub), viz/mcmc_report.py (diagnostic reports), viz/nlsq_plots.py (+1 more)

### Community 422 - "Testfixedparameters / .Test Get Fixed Pa"
Cohesion: 0.22
Nodes (9): Static CMC Config Section (sharding, per_shard_mcmc, validation), FAQ: CMC / Bayesian Questions (when to use, timing, divergence), Glossary Term: CMC (Consensus Monte Carlo), Glossary Term: divergent transitions (NUTS HMC energy errors), Glossary Term: NumPyro (probabilistic programming on JAX), Glossary Term: NUTS (No-U-Turn Sampler), Glossary Term: per-angle mode (auto/constant/individual/fourier), Glossary Term: shard (CMC data partition unit) (+1 more)

### Community 423 - "Testparameteractivestatus / .Test Parame"
Cohesion: 0.22
Nodes (9): Data Handler Architecture (data-handler-architecture.md), ConfigManager (top hub node, 227 edges), HDF5 Format Detection & Loading Pipeline, DatasetOptimizer, homodyne/data/__init__.py, load_xpcs_data(), PhiAngleFilter, PreprocessingPipeline (+1 more)

### Community 424 - "Testoptimizableparameters / .Test Optimi"
Cohesion: 0.25
Nodes (5): Test ValidationResult dataclass., Test valid ValidationResult., Test invalid ValidationResult., Test string representation formatting., TestValidationResult

### Community 425 - "Testvalidationmessages / .Test Failure M"
Cohesion: 0.25
Nodes (5): Test edge cases for parameter info retrieval., Invalid model type should raise ValueError., Parameter info should have all required keys., Parameter counts should be consistent across info fields., TestParameterInfoEdgeCases

### Community 426 - "Testedgecases / .Test Empty Config()"
Cohesion: 0.25
Nodes (5): Verify CMA-ES filters diagonal (t1==t2) points before optimization., Non-diagonal mask must exclude all i==j index pairs., Tiled mask must filter diagonal for every phi angle independently., After filtering, ydata/sigma must have same length as tiled time arrays., TestCMAESDiagonalFiltering

### Community 427 - "Testparametervalidation / .Test Validate"
Cohesion: 0.25
Nodes (7): _compute_g1_shear_core(), Compute shear contribution to g1 using reference implementation approach.      A, Simple vectorization fallback using Python loops., vmap(), Test architectural fix for dispatcher memory allocation (Nov 2025)., Verify meshgrid mode still works for NLSQ (small arrays)., TestDispatcherMemory

### Community 428 - "Main() / Baselinemetrics"
Cohesion: 0.25
Nodes (5): Test the gradient sanity check feature., Test that gradient check detects zero gradient correctly., Test that gradient check detects non-zero gradient correctly., Test that threshold of 1e-10 is appropriate., TestGradientSanityCheck

### Community 429 - "Testparallelthreshold / .Test Below Thre"
Cohesion: 0.25
Nodes (5): Ensure phi_0 is never used (should be phi0)., Ensure gamma_dot_offset is never used (should be gamma_dot_t_offset)., Tests that specifically prevent the gamma_dot_0 vs gamma_dot_t0 bug., Ensure gamma_dot_0 is never used (should be gamma_dot_t0)., TestRegressionPrevention

### Community 430 - "Main() / Main.Py"
Cohesion: 0.25
Nodes (5): Test fixed parameters functionality., Test getting fixed parameters when none specified., Test getting fixed parameters from configuration., Test handling of invalid fixed_parameters type., TestFixedParameters

### Community 431 - ". Check Pressure Levels() / . Trigger Wa"
Cohesion: 0.25
Nodes (5): Test type constants from types.py., Test STATIC_PARAM_NAMES constant., Test LAMINAR_FLOW_PARAM_NAMES constant., Test PARAMETER_NAME_MAPPING constant., TestTypeConstants

### Community 432 - "Optimizationexecutor / .Test Executor Is"
Cohesion: 0.25
Nodes (5): Test validation result messages., Test message for successful validation., Test message for failed validation., Test parameters_checked field., TestValidationMessages

### Community 433 - ".Test Repr() / .Test Config Summary()"
Cohesion: 0.25
Nodes (5): Test edge cases and error handling., Test requesting bounds for unknown parameter., Test with empty configuration., Test with malformed bounds in config., TestEdgeCases

### Community 434 - ".Compute C2() / .Plot Simulated Data()"
Cohesion: 0.25
Nodes (5): Test is_parameter_active() functionality., Test parameter active status without configuration., Test parameter active status with fixed parameters., Test parameter active status with name mapping., TestParameterActiveStatus

### Community 435 - "Testcmaesdiagonalfiltering / .Test Diago"
Cohesion: 0.25
Nodes (5): Test ParameterManager initialization., Test initialization without configuration., Test initialization with configuration., Test initialization with static mode., TestParameterManagerInit

### Community 436 - "Vmap() / Testdispatchermemory"
Cohesion: 0.25
Nodes (5): Test get_optimizable_parameters() functionality., Test optimizable parameters when nothing is fixed., Test optimizable parameters with some fixed., Test optimizable parameters when all are fixed., TestOptimizableParameters

### Community 437 - "Testdataloadingintegration / .Test Compl"
Cohesion: 0.25
Nodes (5): Test INFO-level physics notifications (noteworthy but acceptable)., Test INFO for alpha near zero (normal diffusion)., Test INFO for gamma_dot_t0 < 1e-6., Test INFO for phi0 outside [-10, 10] degrees., TestInfoLevelViolations

### Community 438 - "Testhelptextdocumentation / .Test Cmc Gr"
Cohesion: 0.25
Nodes (5): Test parameter validation integration., Test validation with valid parameters., Test validation with out of bounds parameters., Test that validation uses configuration bounds., TestParameterValidation

### Community 439 - ".Test Mcmc Chains Validation() / .Test M"
Cohesion: 0.29
Nodes (5): Determine if parallel accumulation is worthwhile.      Parameters     ----------, should_use_parallel_accumulation(), Tests for parallel chunk accumulation in NLSQ streaming., Test parallel activation threshold., TestParallelThreshold

### Community 440 - "Testhelptextvalidation / .Test Cmc Group"
Cohesion: 0.25
Nodes (5): T016: Tests for CLI --quiet flag (User Story 1)., --quiet flag shows only ERROR level messages., --quiet flag sets ERROR console level., --quiet takes precedence over --verbose when both specified., TestCLIQuietFlag

### Community 441 - "Testshellaliasdefinitions / .Test Shell "
Cohesion: 0.25
Nodes (4): Check memory pressure levels and trigger responses.          Only logs state tra, Trigger warning-level memory pressure response., Trigger critical-level memory pressure response., Trigger recovery-level response when pressure decreases.

### Community 442 - "Testcmcspecificoptions / .Test All Cmc O"
Cohesion: 0.25
Nodes (5): Test fixed_parameters filtering functionality., Test that fixed_parameters are excluded from initial parameters., Test fixed_parameters with config name mapping., Test combination of active_parameters and fixed_parameters., TestFixedParametersFiltering

### Community 443 - "Testqualitymetrics / Test Result Builder"
Cohesion: 0.25
Nodes (5): Tests for ParameterSpace.from_defaults() class method., Test creating static parameter space from defaults., Test creating laminar flow parameter space from defaults., Test that default priors are reasonably wide., TestParameterSpaceFromDefaults

### Community 444 - "Testnlsqadapterbase / .Test Is Abstract "
Cohesion: 0.25
Nodes (5): Test complex edge case scenarios combining multiple issues., Test all parameters at their minimum bounds., Test all parameters at their maximum bounds., Test midpoint calculation with infinite bounds., TestComplexIntegrationEdgeCases

### Community 445 - "Testsetupbounds / .Test Setup Bounds Fro"
Cohesion: 0.25
Nodes (5): Test that _validate_input validates array dimensions., Test that _validate_input rejects mismatched array lengths., Test that shared methods work correctly., Test that _prepare_data returns structured data., TestSharedMethodImplementation

### Community 446 - "Test Adapter Base.Py / Testadapterinheri"
Cohesion: 0.25
Nodes (5): Tests for NLSQAdapterBase (T057).  Tests the abstract base class for NLSQ adapte, Test that adapters inherit from NLSQAdapterBase., Test that NLSQAdapter inherits from NLSQAdapterBase., Test that NLSQWrapper inherits from NLSQAdapterBase., TestAdapterInheritance

### Community 447 - "Testsharedmethodimplementation / Test Th"
Cohesion: 0.25
Nodes (5): Tests for _compute_covariance() method., Covariance is computed from Jacobian., Covariance computed with sufficient degrees of freedom., Singular Jacobian returns None covariance., TestComputeCovariance

### Community 448 - "Testcomputecovariance / Covariance Is Co"
Cohesion: 0.25
Nodes (5): Tests for _setup_bounds() method., Default bounds are (-inf, inf)., Bounds are set from dictionary., Custom default bounds are applied., TestSetupBounds

### Community 449 - "Testboundsformatconversion / .Test None "
Cohesion: 0.25
Nodes (5): Tests for NLSQAdapterBase abstract class., NLSQAdapterBase cannot be instantiated directly., fit() must be implemented by subclasses., Subclass implementing fit() can be instantiated., TestNLSQAdapterBase

### Community 450 - "Testdataflattening / .Test Empty Data Ha"
Cohesion: 0.29
Nodes (6): OptimizationExecutor, Abstract base class for optimization strategy executors.      Implements the Str, Tests for OptimizationExecutor abstract base class., Test that OptimizationExecutor cannot be instantiated directly., Test that concrete executors implement required methods., TestOptimizationExecutorInterface

### Community 451 - "Create Disabled Filtering Config() / .Te"
Cohesion: 0.25
Nodes (5): Tests for module __all__ exports., InputValidator module exports all expected symbols., ResultValidator module exports all expected symbols., Validation package exports key classes., TestModuleExports

### Community 452 - "Testnlsqconfigisvalid / Test Default Con"
Cohesion: 0.25
Nodes (5): Test HomodyneModel convenience methods., Test config_summary property., Test string representation., Test plot_simulated_data without generating plots., TestHomodyneModelConvenienceMethods

### Community 453 - "Test Nlsq Config.Py / Testnlsqconfigvali"
Cohesion: 0.25
Nodes (4): Compute C2 correlation function using stored configuration.          This high-l, Compute C2 correlation function for a single angle.          Convenience method, Generate and optionally plot simulated C2 data.          This convenience method, Generate heatmap plots for C2 data.

### Community 454 - "Scaling Utils.Py / Compute Averaged Scal"
Cohesion: 0.25
Nodes (5): Test that help text properly documents CMC options., Test that --method help text mentions mcmc option., Test that CMC argument group has a descriptive title., Test that epilog documents CMC sharding options., TestHelpTextDocumentation

### Community 455 - "Testcmcresultmethods / .Test Get Posteri"
Cohesion: 0.25
Nodes (5): Test shell alias definitions in completion.sh., Test that shell aliases are defined in completion.sh., Test that deprecated aliases are not defined., Test that alias descriptions properly document the changes., TestShellAliasDefinitions

### Community 456 - "Teststage2Robustconsensus / .Test Class "
Cohesion: 0.25
Nodes (5): Test help text properly documents CLI options.      Note: Auto-selection tests r, Test that help text shows only nlsq and mcmc as choices., Test that CMC argument group exists with proper title., Test that epilog documents CMC options., TestHelpTextValidation

### Community 457 - "Teststage1Numchainsdefault / .Test Defau"
Cohesion: 0.25
Nodes (5): Test CMC-specific CLI options work with --method cmc.      Note: --min-samples-c, Test that --cmc-num-shards is accepted with mcmc method., Test that --cmc-backend is accepted with mcmc method., Test that all CMC sharding options can be used together., TestCMCSpecificOptions

### Community 458 - "Testboundsawarecv / Test Heterogeneity F"
Cohesion: 0.25
Nodes (5): Unit tests for homodyne.optimization.nlsq.result_builder module.  Tests result b, Tests for QualityMetrics dataclass., Test basic QualityMetrics instantiation., Test that n_at_bounds defaults to 0., TestQualityMetrics

### Community 459 - "Testcliquietflag / .Test Quiet Config Va"
Cohesion: 0.29
Nodes (6): Save 3 JSON files: parameters, analysis results, convergence metrics.      This, _save_nlsq_json_files(), Test JSON file creation for parameters, analysis, and convergence., Test that all 3 JSON files are created., Test that JSON content matches expected schema., TestSaveNLSQJSONFiles

### Community 460 - "Testmultiprocessinglogging / .Test With "
Cohesion: 0.25
Nodes (5): End-to-end workflow integration tests., Test complete workflow: load → process → analyze., Test workflow that processes multiple phi angles., Test load_xpcs_data convenience function integration., TestEndToEndWorkflows

### Community 461 - "Testfunctionsignatures / .Test Data Load"
Cohesion: 0.25
Nodes (5): Unit tests for homodyne.optimization.nlsq.config module.  Tests the NLSQConfig d, Test validation error field is updated correctly., Test that _validation_errors is populated after validate()., Test that _validation_errors is updated on each validate() call., TestNLSQConfigValidationErrors

### Community 462 - "Main() / Load Shard()"
Cohesion: 0.25
Nodes (5): Test NLSQConfig.is_valid method., Test default config is valid., Test custom valid config is valid., Test invalid config returns False., TestNLSQConfigIsValid

### Community 463 - "Model() / Test Homodyne Model.Py"
Cohesion: 0.25
Nodes (5): Tests for build_init_values_dict function with out-of-bounds handling., Test that out-of-bounds initial values are clipped in build_init_values_dict., Test that scalar values are broadcast to all phi angles., Test that explicit per-angle values take precedence over scalar., TestBuildInitValuesDict

### Community 464 - ".Build() / Qualitymetrics"
Cohesion: 0.29
Nodes (6): Convert loaded samples to ArviZ InferenceData.      Parameters     ----------, samples_to_arviz(), Tests for samples_to_arviz function., Test basic conversion to ArviZ., Test converted parameters have correct shapes., TestSamplesToArviz

### Community 465 - "Release V2.22.9 / System Overview"
Cohesion: 0.25
Nodes (5): Tests for CMC shard heterogeneity fixes (Feb 2026).  These tests verify the 6 ta, P2-2: CV calculation should use bounds range for near-zero params., D_offset near zero should not trigger false heterogeneity., Parameters with large mean should be unaffected by bounds-aware CV., TestBoundsAwareCV

### Community 466 - "Api: Cli / Cli Data Pipeline"
Cohesion: 0.25
Nodes (5): Fix 6: num_chains default inconsistency., from_dict({}) must default to 4 chains, matching class default., Class default and from_dict default must agree., Explicit num_chains in YAML should override default., TestStage1NumChainsDefault

### Community 467 - "Testing Guide / Contributing Guide"
Cohesion: 0.32
Nodes (7): compute_averaged_scaling(), estimate_contrast_offset_from_quantiles(), estimate_per_angle_scaling(), Shared scaling utilities for per-angle contrast/offset estimation.  This module, Estimate contrast and offset initial values for each phi angle.      This is the, Compute averaged contrast and offset for constant mode.      This function estim, Estimate contrast and offset from C2 data using physics-informed quantile analys

### Community 468 - "Testnlsqdiagonalmasking / .Test Diagonal"
Cohesion: 0.25
Nodes (5): Fix 4: robust_consensus_mc as default combination method., Default combination method must be robust_consensus_mc., Class-level default must also be robust., Explicit method in YAML should override default., TestStage2RobustConsensus

### Community 469 - "  Init  .Py / Get Optimization Info()"
Cohesion: 0.36
Nodes (7): BaselineMetrics, generate_synthetic_data(), main(), Container for CMC baseline metrics., Generate synthetic XPCS-like data for benchmarking., Run a baseline benchmark and capture metrics., run_baseline_benchmark()

### Community 470 - "Teststage4Constantaveragedscaling / .Tes"
Cohesion: 0.25
Nodes (5): Test data flattening transformation (T006)., Verify multi-dimensional XPCS data (n_phi, n_t1, n_t2) → flattened 1D arrays., Verify meshgrid uses indexing='ij' to preserve correct ordering.          This e, Test graceful handling of empty data., TestDataFlattening

### Community 471 - "Testbuildinitvaluesdict / .Test Constant"
Cohesion: 0.25
Nodes (5): Test bounds format conversion (T010)., Verify homodyne bounds tuple format → NLSQ format conversion.          Test: (lo, Verify bounds validation checks lower < upper elementwise., Test handling of None bounds (unbounded optimization)., TestBoundsFormatConversion

### Community 472 - "N Workers() / Result Queue()"
Cohesion: 0.38
Nodes (6): build_init_dict(), load_shard(), main(), One-off helper to probe laminar CMC log-density at chosen inits.  Usage (from re, Load cached C2 and build a single-shard slice matching CMC prep.      Returns di, Fill missing init values with midpoint of bounds, converted to z-space.      xpc

### Community 473 - ".  Init  () / . Determine Mode()"
Cohesion: 0.29
Nodes (5): model(), Unit Tests for HomodyneModel Hybrid Architecture ===============================, Test HomodyneModel compatibility with legacy CombinedModel., Test that HomodyneModel gives same results as CombinedModel., TestHomodyneModelVsLegacy

### Community 474 - ".Log Summary() / .Compute Regularization"
Cohesion: 0.29
Nodes (7): Release v2.22.9, Data Preparation & Sharding, XPCS Data Loading, System Overview, Trust-Region Levenberg-Marquardt, TestPrefetchLoader, Ground Truth Recovery Accuracy Test

### Community 475 - "Order() / From Dict()"
Cohesion: 0.33
Nodes (7): Contributing Guide, Developer Guide Index, Parameter Bounds Verification, Parameter Registry and Validators, JAX Debugging Techniques (disable_jit, log_compiles), Test Organization (unit/smoke/fast/all suites), Testing Guide

### Community 476 - "  Init  .Py / Get Completion Script()"
Cohesion: 0.33
Nodes (4): Test that physics functions depend on input parameters.      Historical Context:, Test that changing parameters produces different g2 output.          Note: Uses, Test that gradient of g2 with respect to parameters is non-zero., TestParameterDependency

### Community 477 - "Testbackwardcompatibility / .Test Existi"
Cohesion: 0.33
Nodes (4): Test string representation with fixed parameters., Test repr includes fixed parameter count., Test repr with no fixed parameters., TestReprWithFixedParams

### Community 478 - "Data Pipeline.Py /  Pool Mcmc Data()"
Cohesion: 0.33
Nodes (4): Test parameter name mapping., Test gamma_dot_0 -> gamma_dot_t0 mapping., Test phi_0 -> phi0 mapping., TestParameterNameMapping

### Community 479 - ".Get Memory Stats() / .Get Pressure Tren"
Cohesion: 0.33
Nodes (5): get_optimization_info(), JAX-First Optimization for Homodyne.4 ==========================================, # NOTE: DatasetSizeStrategy, OptimizationStrategy, estimate_memory_requirements, Get information about available optimization methods.      Returns     -------, # NOTE: DatasetSizeStrategy, OptimizationStrategy, estimate_memory_requirements

### Community 480 - "Allocationerror / . Allocate Buffer()"
Cohesion: 0.33
Nodes (5): get_completion_script(), get_xla_config_script(), Shell completion and activation scripts for homodyne.  This subpackage contains, Get the path to the bash completion script.      Returns:         Absolute path, Get the path to the XLA configuration script.      Args:         shell: Shell ty

### Community 481 - "Test Executors.Py / Testexecutorerrorhan"
Cohesion: 0.33
Nodes (4): T015: Tests for CLI --verbose flag (User Story 1)., --verbose flag enables DEBUG level console logging., --verbose flag uses detailed console format., TestCLIVerboseFlag

### Community 482 - ".Test Very Small Dt() / .Test Single Tim"
Cohesion: 0.33
Nodes (3): Get human-readable pressure level., Get memory pressure trend over specified window.          Args:             wind, Get comprehensive memory statistics.

### Community 483 - "Testjaxbackendfallback / .Test Numpy Com"
Cohesion: 0.4
Nodes (4): AllocationError, Raised when memory allocation fails., Allocate new memory buffer with tracking., Allocate virtual memory-backed array for very large datasets.

### Community 484 - "Testparameterdependency / .Test G2 Gradi"
Cohesion: 0.33
Nodes (4): Test that parameter space loading doesn't introduce regressions., Verify ParameterSpace.from_config() correctly loads priors.          Tests that, Verify initial values always satisfy parameter bounds.          Tests that mid-p, TestParameterSpaceLoadingRegression

### Community 485 - "Testconstants / .Test Pi Value()"
Cohesion: 0.33
Nodes (4): Unit tests for homodyne.optimization.nlsq.strategies.executors module.  Tests op, Tests for error handling in executors., Test that StandardExecutor propagates optimization errors., TestExecutorErrorHandling

### Community 486 - "Testconfigfilevalidation / .Test Missing"
Cohesion: 0.33
Nodes (4): Test edge cases and error handling., Test with single time point., Test with very small dt value., TestHomodyneModelEdgeCases

### Community 487 - "Testconflictingarguments / .Test Verbose"
Cohesion: 0.33
Nodes (4): Tests for NLSQ residual diagonal masking (v2.14.2+).      The unified diagonal h, Test the concept of diagonal masking for residuals., Test that diagonal mask affects chi-squared correctly., TestNLSQDiagonalMasking

### Community 488 - "Testdefaultconfigbehavior / Test Default"
Cohesion: 0.33
Nodes (4): Test backward compatibility of CLI integration., Test existing CLI usage without CMC arguments still works., Test --method cmc without CMC arguments works (auto-selection)., TestBackwardCompatibility

### Community 489 - "Testclihelpoutput / .Test Homodyne Help "
Cohesion: 0.33
Nodes (4): Test default configuration behavior., Test that default config path is ./homodyne_config.yaml., Test that default output directory is ./homodyne_results., TestDefaultConfigBehavior

### Community 490 - "Testmethodvalidation / .Test Validate Ar"
Cohesion: 0.33
Nodes (4): Test actual CLI help output contains expected information., Test that homodyne --help shows method choices., Test that homodyne --help does not mention deprecated methods., TestCliHelpOutput

### Community 491 - "Create Overlapping Ranges Config() / .Te"
Cohesion: 0.33
Nodes (4): Test handling of conflicting arguments., Test that --static-mode and --laminar-flow conflict., Test that --verbose and --quiet conflict., TestConflictingArguments

### Community 492 - "Scaling.Py / Log Scaling Factors()"
Cohesion: 0.33
Nodes (4): Test module constants., Test PI constant is correct., Test EPS constant is appropriate., TestConstants

### Community 493 - "Testmodelnumshardsparameter / .Test Aver"
Cohesion: 0.33
Nodes (5): log_scaling_factors(), Parameter Scaling for MCMC Gradient Balancing.  This module implements non-cente, # NOTE: use_log_space is intentionally ignored for now., # NOTE: use_log_space is intentionally ignored for now., Log scaling factors for debugging.      Parameters     ----------     scalings :

### Community 494 - ".  Init  () /  Fakecmcresult"
Cohesion: 0.33
Nodes (4): Test that model functions accept and use num_shards., xpcs_model_averaged accepts num_shards kwarg without error., xpcs_model_constant accepts num_shards kwarg without error., TestModelNumShardsParameter

### Community 495 - "Test Plots.Py / Testnlsqplotscontrastwar"
Cohesion: 0.33
Nodes (3): Persistent worker pool for CMC shard processing.  Spawns N persistent worker pro, Persistent worker event loop.      Processes tasks until a None sentinel is rece, _worker_event_loop()

### Community 496 - "Testcliverboseflag / .Test Verbose Enabl"
Cohesion: 0.4
Nodes (3): _FakeCMCResult, Tests for CMC c2_fitted computation wiring., test_compute_fitted_c2_uses_unique_phi()

### Community 497 - "Testreturntypes / Test Compatibility.Py"
Cohesion: 0.33
Nodes (4): Tests for visualization validation and basic plot functions., Test that low contrast logs a warning instead of overriding., Very low contrast should log a warning, not silently override., TestNlsqPlotsContrastWarning

### Community 498 - "Testdeprecationwarnings / Test Deprecati"
Cohesion: 0.33
Nodes (3): Initialize Fourier reparameterizer.          Parameters         ----------, Determine whether to use Fourier mode.          Returns         -------, Compute Fourier basis matrix B where values = B @ coeffs.          Returns

### Community 499 - "Testrealdatastratification / Test Real D"
Cohesion: 0.33
Nodes (3): create_fourier_model_wrapper(), Fourier Reparameterization for Anti-Degeneracy Defense.  This module replaces n_, Create a model function wrapper that handles Fourier conversion.      The wrappe

### Community 500 - "Main() / Compute C2 Cmc()"
Cohesion: 0.33
Nodes (3): Compute regularization term to add to loss.          Parameters         --------, Check if CV exceeds max_cv threshold.          Parameters         ----------, Log regularization summary.          Parameters         ----------         param

### Community 501 - "Manager.Py / Get Logger()"
Cohesion: 0.33
Nodes (4): Test manual NLSQ → MCMC workflow with parameter copying., Test full workflow: NLSQ → manual copy → MCMC.          v2.4.0: Per-angle scalin, Test that initial_parameters structure unchanged from v2.0., TestManualNLSQMCMCWorkflow

### Community 502 - ".To Dict() / Memoryprofile"
Cohesion: 0.33
Nodes (4): Test auto-retry mechanism and error handling., Test auto-retry with different random seeds (max 3 retries)., Test that invalid method names raise clear errors., TestConvergenceAndErrorHandling

### Community 503 - "Sample Result() / Test Results.Py"
Cohesion: 0.33
Nodes (4): Test that CMC automatic selection preserves MCMC convergence quality., Verify CMC produces valid combined R-hat and ESS.          When CMC runs success, Verify NUTS and CMC modes produce equivalent convergence quality.          For s, TestCMCConvergencePreservation

### Community 504 - "Meshgrid Lru Cache / Jax Computational K"
Cohesion: 0.33
Nodes (4): Real Data Validation for Stratified Chunking  Tests the stratification implement, Validate stratification on real experimental data., Test memory estimation with realistic dataset sizes., TestRealDataStratification

### Community 505 - "L() / N()"
Cohesion: 0.47
Nodes (5): compute_c2_cmc(), load_nlsq_results(), main(), Load NLSQ results from directory., Compute C2 using CMC physics.      Returns C2 heatmap with shape (n_phi, n_times

### Community 506 - "Analysis Modes (Static, Laminar Flow) / "
Cohesion: 0.33
Nodes (5): NLSQ Optimization Subpackage for Homodyne.  This subpackage contains all NLSQ (N, # NOTE: Subsampling is explicitly NOT supported per project requirements., # NOTE: DatasetSizeStrategy, OptimizationStrategy, estimate_memory_requirements, # NOTE: No subsampling - numerical precision takes priority, # NOTE: DatasetSizeStrategy, OptimizationStrategy, estimate_memory_requirements

### Community 507 - "Yaml Template: Homodyne Laminar Flow.Yam"
Cohesion: 0.33
Nodes (6): Four Scaling Modes: auto/constant/individual/fourier, Anti-Degeneracy Defense System (Theory), Fourier Basis Matrix B for Per-Angle Conversion, Constant Mode: 9 Parameters (7 physical + 2 averaged scaling), Fourier Reparameterization for Per-Angle Scaling, FourierReparameterizer Class

### Community 508 - ".  Init  () / Filtercriteria"
Cohesion: 0.4
Nodes (3): load_xpcs_config(), Minimal Configuration Management for Homodyne ==================================, Load XPCS configuration from file.      Convenience function for loading configu

### Community 510 - ".To Dict() / .Save Provenance()"
Cohesion: 0.4
Nodes (4): mock_parameter_space(), Integration tests for CMC reparameterization., Create parameter space for laminar_flow mode., test_reparameterized_model_produces_valid_samples()

### Community 511 - ".Log Summary() / .Get Diagnostics()"
Cohesion: 0.4
Nodes (5): Hybrid Architecture Wrapper, JAX Computational Kernels, Meshgrid LRU Cache, Eager Factor Pre-computation, Theory Engine Orchestrator

### Community 512 - ".Per Angle To Fourier() / .Get Initial C"
Cohesion: 0.6
Nodes (3): l(), n(), s()

### Community 514 - "Mcmc Dashboard.Py / Plot Cmc Summary Das"
Cohesion: 0.5
Nodes (3): _PhaseRecord, Internal record for phase timing., Mark phase start for timing.          Args:             name: Phase name (e.g.,

### Community 515 - "Testcmcwarningswithnlsq / .Test Cmc Opti"
Cohesion: 0.5
Nodes (3): plot_cmc_summary_dashboard(), MCMC Summary Dashboard Visualization.  Provides a comprehensive multi-panel CMC, Create comprehensive multi-panel CMC summary dashboard.      Combines all diagno

### Community 516 - "Args Parser.Py / Create Parser()"
Cohesion: 0.5
Nodes (3): plot_posterior_comparison(), MCMC Posterior Comparison Visualization.  Provides per-shard vs combined posteri, Compare per-shard posteriors with combined posterior (CMC only).      Visualizes

### Community 517 - ".To Dict() / Timingbreakdown"
Cohesion: 0.5
Nodes (4): measure_memory(), MemoryResult, Measure memory usage during function execution.      Parameters     ----------, Memory measurement result.

### Community 518 - ".To Normalized() / . Smooth Bound Invers"
Cohesion: 0.5
Nodes (3): create_parser(), Argument Parser for Homodyne CLI ===================================  Simplified, Create the main argument parser for Homodyne CLI.      Returns:         Configur

### Community 520 - " Phaserecord / .Start Phase()"
Cohesion: 0.5
Nodes (3): pytest_collection_modifyitems(), Integration test configuration., Auto-apply integration marker to all tests in this directory.

### Community 523 - ".Test Basic Usage Example() / Testdocume"
Cohesion: 0.5
Nodes (3): API test fixtures — lightweight overrides for interface contract tests.  API com, Minimal synthetic data for API contract tests.      10x10x3 (300 elements) vs ma, synthetic_xpcs_data()

### Community 524 - "Sub-Diffusion (0 < Alpha < 1) / Classica"
Cohesion: 0.5
Nodes (4): Classical Stochastic Processes, Langevin Equation (Overdamped), Ornstein-Uhlenbeck Process (Sub-Diffusion), Sub-Diffusion (0 < alpha < 1)

### Community 538 - "Consensus Monte Carlo / Precompute Shard"
Cohesion: 0.67
Nodes (3): Consensus Monte Carlo, Non-Linear Least Squares, precompute_shard_grid

## Knowledge Gaps
- **6331 isolated node(s):** `Cleanup utilities for homodyne package.  This module provides utilities to remov`, `A file or directory to clean up.`, `Get the virtual environment path if in one.      Returns:         Path to venv o`, `Find all homodyne-related files that can be cleaned up.      Returns:         Li`, `Remove shell completion files.      Args:         dry_run: If True, don't actual` (+6326 more)
  These have ≤1 connection - possible missing edges or undocumented components.
- **519 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 `NLSQWrapper` connect `Test Fixtures & Process Utilities` to `Result Serialization & Messaging`, `Testnlsqwrappererrorhandling / .Test Err`, `Test Sphinx Rst Formatting() / Test Conf`, `Testmeshgridcache / Reset Cache Stats()`, `Main() / Compute C2 Cmc()`, `JAX JIT / vmap Primitives`, `CMC Data Prep & Sharding`, `Cmc Prior Tempering / Gradient-Safe Floo`, `.Copy() / .  Str  ()`, `Test Streaming Optimizer.Py / Test Confi`, `.  Init  () / .Get Bounds()`, `Jit() / Grad()`, `Testjaxbackendedgecases / .Test Jit Comp`, `Physics Params() / Testcmcphysicsvalues`, `Testunifiedmoduleapi / Get Available Bac`, `.Test Diagnostics() / .Test Reset Clears`, `Jit() / Grad()`, `.Test Str() / .Test Repr()`, `Main() / Baselinemetrics`, `Testparallelthreshold / .Test Below Thre`, `.Test Summary Values() / Testcmcresulted`, `Nlsqresult / .  Init  ()`, `.Test Boundary Tolerance() / .Test Multi`, `.Test Both Transforms() / .Test D Ref Tr`, `.Test Single Angle() / .Test Laminar Flo`, `Protocol / .Compute G2()`, `Testsetupbounds / .Test Setup Bounds Fro`, `Test Adapter Base.Py / Testadapterinheri`, `Testsharedmethodimplementation / Test Th`, `Testextractnlsqmetadata /  Extract Nlsq `, `Testboundsformatconversion / .Test None `, `Testcomputecovariance / Covariance Is Co`, `Testvalidateinput / Nan In T1 Raises Val`, `Testnlsqwrapperinit / .Test Wrapper Init`, `Parser() / Mock Config()`, `.With Info() / Resultbuilder`, `Testcmcresult / .Test Ess Values()`, `Test Logging.Py / Testwithcontextshard`, `Main() / Cpu Optimization.Py`, `.  Init  () / .Snapshot()`, `Teststage4Constantaveragedscaling / .Tes`, `Testbuildinitvaluesdict / .Test Constant`, `.Test Symmetry() / .Test Non Negative()`, `Testvalidationcomponentedgecases / .Test`, `.  Init  () / Inputvalidator`, `.Test Wavevector T1 T2 Unchanged() / .Te`, `Testmoduleexports / Test Nlsq Validation`, `Mock Data() / Mock Result()`, `.  Init  () / Parameterspace`, `Testoptimizationstrategy / .Test Strateg`, `Logconfiguration / Worker Function()`, `.Test Get Prior Means() / .Test Get Boun`, `Test Residual Function.Py / Testresidual`, ` Apply Cli Overrides() / Test Overriding`?**
  _High betweenness centrality (0.191) - this node is a cross-community bridge._
- **Why does `ParameterManager` connect `Nlsqresult / .  Init  ()` to `Test Fixtures & Process Utilities`, `.Test Success False Failed() / Determine`, `Test Mock Fixtures`, `Testoptimizationresult / .Test Result Ha`, `.Fit() / Adapter.Py`, `Model.Py / Xpcs Model Averaged()`, `Test Streaming Optimizer.Py / Test Confi`, `.  Init  () / .Get Bounds()`, `Jit() / Vmap()`, `.  Init  () / Testcaching`, `.Test Str() / .Test Repr()`, `Main() / Main.Py`, `. Check Pressure Levels() / . Trigger Wa`, `Optimizationexecutor / .Test Executor Is`, `.  Init  () / Testestimatephysicalworker`, `.Test Repr() / .Test Config Summary()`, `Testcmaesdiagonalfiltering / .Test Diago`, `.Compute C2() / .Plot Simulated Data()`, `Protocol / .Compute G2()`, `Testhelptextdocumentation / .Test Cmc Gr`, `Model Func() / Testjitcompilation`, `Vmap() / Testdispatchermemory`, `Testdataloadingintegration / .Test Compl`, ` Echo Worker() /  Error Worker()`, `From Dict() / Is Enabled()`, `Log Exception() / Testlogexception`, `Test Api Documentation.Py / Test Core Mo`, `Compute Uncertainties() / Testcomputeunc`, `.With Info() / Resultbuilder`, `Testnlsqwrapperfit / .Test Fit Logs Iter`, `Testbackwardcompatibility / .Test Existi`, `Data Pipeline.Py /  Pool Mcmc Data()`, `Testdtpropagation / Testtimegridgenerati`, `.Validate All() / Input Validator.Py`, `.  Repr  () / Homodynemodel`, `Path Validation.Py / Testsanitizelogpath`, `.Test Security Edge Cases() / .Test Vali`, `Testdevicebenchmarking / Benchmark Devic`, `.Test Shear Rate Alias() / .Test Trapezo`?**
  _High betweenness centrality (0.101) - this node is a cross-community bridge._
- **Why does `ConfigManager` connect `.Fit() / Adapter.Py` to `Test Sphinx Rst Formatting() / Test Conf`, `Testyamlescapestring /  Yaml Escape Stri`, `Datasetmetadata / .Create 1B Dataset()`, `Syntheticxpcsdata / Synthetic Data.Py`, `.As Dict() /  Json Safe()`, `Teststage3Shardsize /  Resolve Max Point`, `Memorypool / .Get Buffer()`, `Test Streaming Optimizer.Py / Test Confi`, `Samplingplan / Reparamconfig`, `.To Dict() / Fit Quality.Py`, `Jit() / Vmap()`, `.  Init  () / Testcaching`, `Log Calls() / Log Phase()`, `Testcpudetection / Benchmark Cpu Perform`, `Gradientresult / Numpy Hessian()`, `Nlsqresult / .  Init  ()`, `Protocol / .Compute G2()`, `Config.Py / Get Logger()`, `Angle In Range() / Angle Filtering.Py`, `Testparamcountbymode / Testgetmodelparam`, `Testcmcspecificoptions / .Test All Cmc O`, `Testqualitymetrics / Test Result Builder`, `Testcmcargumentvalidation / .Test Valid `, `Testnlsqadapterbase / .Test Is Abstract `, `Compute Uncertainties() / Testcomputeunc`, `Get Executor() / Testgetexecutor`, `Testjaxarraycreation / .Test Meshgrid Cr`, `.Test Method Mcmc Accepted() / .Test Met`, `.Fit() / .Check()`, `.Test Scalar Layout Expanded() / Testext`, `Main() / .Log()`, `Testcmcoptions / .Test Cmc Options Warne`, `Synthetic C2 Data() / Testnlsqperformanc`, `Scaling Utils.Py / Compute Averaged Scal`, `Testcmcresultmethods / .Test Get Posteri`, `Teststage1Numchainsdefault / .Test Defau`, `.With Info() / Resultbuilder`, `Test Cli Commands.Py / Testconfiggenerat`, `Teststage2Robustconsensus / .Test Class `, `Validation.Py / Validate Plot Arrays()`, `Testpublicapistability / .Test Core Api `, `Testcliquietflag / .Test Quiet Config Va`, `Sequential.Py /  Jax Jacobian()`, `Enable D Total() / Enable Log Gamma()`, `Mockchunk / Mockchunkeddata`, `N Workers() / Result Queue()`, `.Close() / .Close()`, `.To Dict() / From Dict()`, `.Test Zeros Matrix() / .Test Uniform Val`, `.Test Zero D0() / .Test Positive Output(`, `Sample Result() / Test Results.Py`, `Testmethodargumentparsing / .Test Method`, `.Test Good Quality Fit() / .Test Poor Qu`, `Testnlsqadapterbase / .Test Adapter Base`, `Testparameterdependency / .Test G2 Gradi`, `Testdefaultconfigbehavior / Test Default`, `Testclihelpoutput / .Test Homodyne Help `, `Testmethodvalidation / .Test Validate Ar`, `Create Overlapping Ranges Config() / .Te`, `.Test All Inf Array() / Test Viz Validat`, `Testcompletionaliases / .Test Aliases Pr`, `Manager.Py / Get Logger()`, `.To Dict() / Memoryprofile`, `Physics Utils.Py / Testcalculateshearrat`, `Testdeprecatedmethodrejection / .Test Me`, `Testprepareparameterdata /  Prepare Para`, `Testgetphysicalparamcount / Get Physical`, `Testbuildresult / Tests For  Build Resul`, `.  Init  () / Filtercriteria`, `Finite Parameters Pass. / .Test Inf Para`?**
  _High betweenness centrality (0.100) - this node is a cross-community bridge._
- **Are the 199 inferred relationships involving `ConfigManager` (e.g. with `ParameterManager` and `NLSQResult`) actually correct?**
  _`ConfigManager` has 199 INFERRED edges - model-reasoned connections that need verification._
- **Are the 158 inferred relationships involving `NLSQWrapper` (e.g. with `ParameterManager` and `NumericalValidator`) actually correct?**
  _`NLSQWrapper` has 158 INFERRED edges - model-reasoned connections that need verification._
- **Are the 162 inferred relationships involving `ParameterManager` (e.g. with `ValidationResult` and `ParameterSpace`) actually correct?**
  _`ParameterManager` has 162 INFERRED edges - model-reasoned connections that need verification._
- **Are the 136 inferred relationships involving `ValueError` (e.g. with `precompute_shard_grid()` and `compute_g1_diffusion()`) actually correct?**
  _`ValueError` has 136 INFERRED edges - model-reasoned connections that need verification._