v0.1.0

JuliaBUGS v0.1.0

Closed issues:

• Add a lot of test models (#1)
• Actual parser -- external language? (#2)
• Document BUGS syntax that is difficult to support via Julia macro (#3)
• String manipulation to convert BUGS code into Julia AST? (#4)
• Support interpolation in @bugsast (#5)
• Use pattern matching (#6)
• Support incremental construction of GraphInfo (#16)
• Interesting package that might help implement our BUGS parser (#7)
• Transform syntax errors (#8)
• Type checking at IR level instead of AST level (#9)
• Roadmap to going public (#11)
• Review Readme and other old files lying around; clean up (#12)
• @bugsmodel_str doesn't support multiple-line expressions (#13)
• Documentation Checklist (#14)
• Fix the example in README (#17)
• Fix function identifier conflicts and precompilation (#18)
• Separate model construction and conditioning of toturing. (#19)
• Disallowing using stochastic variables as loop bounds/indices(even when they have observed values). (#20)
• Warn user about BUGS-style link function syntax. (#21)
• Only stochastic variable is reported in MCMCChain summury (#25)
• Setting up CI workflows for docs, tests and formating. (#26)
• Compile BUGS model to multiple Turing models / Distributions to enable Gibbs sampling (#28)
• Additional compilation target: LogDensityProblems (#30)
• More Julian syntax (#31)
• Verify the BUGS distribution functions in primitives.jl are correct. (#32)
• Add logdensity correctness tests for all BUGS example models (#39)
• Add support for DataFrames.jl (#42)
• Add LogdensityProblemsAD extension (#49)
• Update README for the new parse and compile function (#54)
• Implement AbstractMCMC.bundle_samples for MCMC samples conversion (#63)

Merged pull requests:

• Steps towards a functional compiler from Bugs to GraphPPL. (#10) (@phipsgabler)
• Towards the first public release. (#15) (@sunxd3)
• Fixed a small typo. (#22) (@yebai)
• Remove Turing dependency. (#23) (@sunxd3)
• Improve documentations. (#24) (@sunxd3)
• Stochastic indexing (#29) (@yebai)
• Formatting and improve docs. (#33) (@sunxd3)
• Fix bugs related to stochastic indexing. (#34) (@sunxd3)
• Fix link function syntax in tests. (#35) (@yebai)
• Fix testCI fails. (#36) (@sunxd3)
• More efficient dependency graph based compiler for BUGS (#37) (@yebai)
• LogDensityProblems target (#38) (@sunxd3)
• Fix errors to successfully compile and compute logdensity for all examples from Volume 1. (#41) (@sunxd3)
• Global variable store (#43) (@yebai)
• Some tiny fix (#44) (@sunxd3)
• Update docstrings for distributions (#45) (@sunxd3)
• Raise Julia version to 1.8 (#46) (@sunxd3)
• Improve docs (#47) (@sunxd3)
• Some refactoring (#48) (@sunxd3)
• Testing and bugs fixes with DynamicPPL (#50) (@sunxd3)
• Fix name clash for test models. (#51) (@yebai)
• Add a parser for BUGS (#52) (@sunxd3)
• Some optimization to the compilation time (#53) (@sunxd3)
• Update parser.md (#55) (@yebai)
• Markov Blanket Interface and some other minor fixes. (#56) (@sunxd3)
• Add link to BUGS syntax BNF definition (#57) (@yebai)
• Fix Typos in ReadMe (#58) (@ParadaCarleton)
• Update README.md (#60) (@yebai)
• Some minor improvements of README (#61) (@yebai)
• Switch to ADgradient (#62) (@yebai)
• Remove AuxiliaryNodes from the final graph (#64) (@sunxd3)
• Delete JuliaBUGSMCMCChainsExt.jl (#65) (@yebai)
• Restrict model type for bundle_samples (#67) (@yebai)
• Remove auxiliary nodes plotting from graph extensions. (#68) (@yebai)
• Restrict sampler to subtypes AbstractHMCSampler (#72) (@yebai)
• Improve documentations. (#73) (@sunxd3)
• Structure the folder of SymbolicPPL code and add README (#74) (@sunxd3)
• Update README.md (#75) (@yebai)
• Update graph_plotting.md (#76) (@sunxd3)
• Add compat and license (#77) (@sunxd3)
• Fix upper bounds for dependencies. (#78) (@yebai)
• Switch to inner constructor for MarkovBlanketCoveredBUGSModel (#79) (@sunxd3)