* Add interface, initial integration, working guide for interface. * Merge branch 'master' into csp/interface-pt1 * Initial work on HMC * Added `transitions_init` function * More work. * Add sampler state type. * SMC is working now. * Imports * Allow chains to take kwargs, import Chains function * More work on interface. * Updates for PG * Added default sample_init! for chain resumption * Silenced annoying warning. * Imported the set_resume! function. * Created set_resume! to resume chains. * Tidying up the particle samplers. * MH work. * Typing changes, typo fixes * Interface updates, IS, MH are done, and HMC beginnings. * Fix interface typo * Deleted mistakenly added file. * HMC works, NUTS/HMCDA doesn't. * Added callback functionality to interface. * Fixed spacing. * Initial work on Gibbs. * HMC, NUTS, HMCDA now work with the new interface. * Added an additional ease-of-use interface function for step functions. * Work on Gibbs API updates. * More work on Gibbs. * Set Gibbs to use regular Transition type. * Minor changes. * Fixed PG, SMC. * Add SMC to Gibbs components. * Move contributed samplers to `contrib/inference` folder. * Remove SMC from Gibbs. * Moved PMMH, IPMCMC to contrib folder. * Set up contribution folder. * Move to new function format for HMC. * Link all HMC. * HMC test updates. * link! and invlink! for dynamic HMC parameter initialization. * Fixed variable name updates. * Fixed kwargs bug. * Test updates. * Always call Sampler with `model` * DynamicHMC support. * Allow runmodel! with SampleFromUniform and SampleFromPrior * Misc. updates. * Allowed Gibbs to use the previous transition object. * More specific dispatch for HMC. * Commented out particle samplers that may not be supported. * Test updates. * Fixed type parameter for ParticleTransition * Removed transition allocation for Gibbs step (unused) * HMC updates, moved tests. * Corrected sampler linking. * Test updates, Gibbs fixes. * Improvements to use getparams, updated * fix mapreduce error * fix the fix * Empty space returns all indices now. * Test updates. * Test fixes, improvements to chain construction and VarInfo parameter retrieval. * Test updates. * Test updates (again) * Minor updates to parameter retrieval, name construction. * Minor updates to parameter retrieval, name construction. * Revert "Minor updates to parameter retrieval, name construction." This reverts commit 626d410. * Revert "Merge branch 'master' into csp/interface-pt2" This reverts commit 9a47abc, reversing changes made to cb811e9. * Added istrans function as a shortcut * HMC improvements and test updates. * Test improvements, varname changes. * VarName updates. * Fixed all the VarName stuff, thanks @mohamed82008. * Test fixes. * Fixed gids, idcs lengths. * Moved interface tools into separate file. * Added interfacel.jl * Remove isnothing in favor of x === nothing for compat reasons. * Lower bound MCMCChains. * Update manifest. * Remove another isnothing( ) call. * Cleanup: copied `docs` folder from master. * Cleanup: fixed a few strange git merge errors by hand. * SamplerState => AbstractSamplerState, fixed constructor. * Added VI back in. * Fixed exports * Fixed variational files. * Add sample_init! and step! functions for DynamicHMC * Add VI tests in. * Recover ad.jl changes. * Add ad.jl tests. * Update AdvancedSMC, use an hmc.jl convention. * Add assert statement for resume_from. * Move tonametuple to RandomVariables.jl * Fixed docstring for tonamedtuple * BlankState => SamplerState * Add back changes from #860 * Revert "Add back changes from #860" This reverts commit fedd004. * final_logevidence => average_logevidence * Added comment to _getidcs * Exports and AdvancedSMC removal of weight field. * Test fixes, SMC updates. * Update SMC(n_particles) to just SMC(). * Remove ~isempty check for updategid! * Commenting on Gibbs gid, removed old IS sampler signature. * Consolidate default interface extensions. * Removed old Sample code, removed a comment from RV, updated runtests. * Add distributions.jl tests back in. * Some doc fixes * Fixed a minor bug with chain sections. * Updated interface guide. * Add initialize_theta, remove sample_end for DHMC * Allow parameter initialization for SMC * HMC pass RNG, functionalized parameter init * Convert internals to NamedTuple, add init theta * Updated max tree depth and init_theta * Set NUTS to DiagEuclidian * Allow users to disable the progress meter. * Add a comment to clarify state_bad. * Fixed an overwritten function. * Allow DynamicHMC to use parameter init. * Fixed performance regression in hmc_step * Removed a bad file. * Gibbs updates, HMC fixes? * Added bad AD fix. * Fixed misspelled function. * Reverted HMC performance fix. * update the new AHMC interface * fix interface bug; change tests to use NUTS * rename internal step size for HMCDA and NUTS to simply ϵ (interface unchanged); unify the HMCState initalizer * update AHMC interface * Support AHMC callback, new HamiltonianTransition type. * Allowed use of Turing's global PROGRESS * update name and fix next! bug * Remove InterfaceExtensions.jl * Rename tests for interface implementations. * Fixed runtests.jl. * Bound DynamicHMC to [1.0-2.0) * Lower bound AHMC at 0.2.4 * Delete Manifest. * Removed ref to missing file. * Update incomplete sentence. * Typing DHMC * Ignore manifest. * Minor RandomVariables updates. * Cleaning particle code, parametric typing * Typing Gibbs * Some HMC typing. * Removing getparams * Typing IS and MH * Typing IS * Remove unintentionally added files. * Remove weird comments in test file. * Unbreaking things. * Fixed IS * Fixed DynamicHMC imports. * Switched a compiler test to HMC instead of NUTS. * improve docstring * remove a space * Formatting and tidying. * Add docstring to GibbsState, removed subsamples. * Rename spl_bad and state_bad. * Fixed dim issue, consolidated gen_metric * Remove dim insertion, added update call to hmc.jl. * Added resize! call to sample_init! for HMC. * Fixed preconditioner call bug. * Change TruncatedNormal to Uniform * Remove cache folder. * Tidied AdvancedSMC. * Minor bugfix for SMC. * Add update back to HMC code, add test. * fix adaptor init bug * fix SMC constructor bug (missing type info) * make HMC test more robust * Changed transition to use full struct name. * Remove docs/site * Removed experimental functions. * Style updates, docstring improvements. * Fix Chains constructor bug. * Removed progress kwarg from default callback. * Docstring update. * Allow the use of progress_style=:plain to use the basic progress bar. * increment version number
Original file line number	Diff line number	Diff line change
`@@ -21,3 +21,4 @@ docs/.gems/`
`21`	`21`	`docs/Gemfile.lock`
`22`	`22`
`23`	`23`	`.DS_Store`
	`24`	`+Manifest.toml`