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Reopening of previous PR #309

Merged
merged 262 commits into from
Dec 12, 2021
Merged

Reopening of previous PR #309

merged 262 commits into from
Dec 12, 2021
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Commits on May 31, 2021

  1. fixed some signatures for Model

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  2. fixed a method call

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Commits on Jun 1, 2021

  1. fixed method signatures

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  2. sort of fixed the matchingvalue functionality for model

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  3. formatting

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  4. removed redundant _tilde method

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  5. Merge branch 'tor/tilde-simplification' into tor/sampler-context

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  6. removed left-over acclogp! that should not be here anymore

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  7. export SamplingContext

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  8. use context instead of ctx to refer to contexts

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  9. formatting

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  10. use context instead of ctx for variables

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  11. use context instead of ctx to refer to contexts

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Commits on Jun 2, 2021

  1. Update src/compiler.jl 

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  2. Update src/context_implementations.jl 

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  3. Apply suggestions from code review 

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  4. added some whitespace to some docstrings

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  5. deprecated tilde and dot_tilde plus exported new versions

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  6. formatting 

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  7. Merge branch 'master' into tor/tilde-simplification

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  8. minor version bump

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Commits on Jun 3, 2021

  1. Merge branch 'master' into tor/sampler-context

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Commits on Jun 4, 2021

  1. Merge branch 'master' into tor/sampler-context

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  2. Merge branch 'master' into tor/tilde-simplification

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Commits on Jun 7, 2021

  1. Merge branch 'master' into tor/tilde-simplification

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  2. Merge branch 'tor/tilde-simplification' into tor/sampling-context-simple

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  3. added impl of matchingvalue for contexts

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  4. reverted the change that makes assume always resample

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  5. removed the inds arguments from assume and dot_assume to stay non-bre… 

    …aking
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  6. Update src/context_implementations.jl 

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  7. added missing sampler arg to tilde_observe

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  8. Merge branch 'tor/sampling-context-simple' of github.com:TuringLang/D… 

    …ynamicPPL.jl into tor/sampling-context-simple
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  9. added missing sampler argument in dot_tilde_observe

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  10. fixed order of arguments in some dot_assume calls

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  11. formatting

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  12. formatting

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  13. added missing sampler argument in tilde_observe for SamplingContext

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  14. added missing word in a docstring

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Commits on Jun 8, 2021

  1. updated submodel macro

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  2. removed unwrap_childcontext and related since its not needed for this PR

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  3. updated submodel macro

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  4. fixed evaluation implementations of dot_assume

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  5. updated pointwise_loglikelihoods and related

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  6. added proper tests for pointwise_loglikelihoods

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  7. updated DPPL tests to reflect recent changes

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  8. bump minor version since this will be breaking

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  9. Merge branch 'tor/tilde-simplification' into tor/sampling-context-simple

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  10. formatting

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  11. formatting

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  12. renamed mean_of_mean_models used in tests

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Commits on Jun 9, 2021

  1. bumped dppl version in integration tests

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  2. Apply suggestions from code review 

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  3. Apply suggestions from code review 

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  4. fixed ambiguity error

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  5. Merge branch 'tor/sampling-context-simple' of github.com:TuringLang/D… 

    …ynamicPPL.jl into tor/sampling-context-simple
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  6. Introduction of SamplingContext: keeping it simple (#259) 

    This is #253 but the only motivation here is to get `SamplingContext` in, nothing relating to interactions with other contexts, etc.

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  7. Update src/DynamicPPL.jl 

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  8. Merge branch 'master' into tor/tilde-simplification

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  9. Merge branch 'tor/tilde-simplification' into tor/simple-varinfo-v2

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Commits on Jun 10, 2021

  1. added initial impl of SimpleVarInfo

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  2. remove unnecessary debug statements to be compat with Zygote

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  3. make reconstruct slightly more generic

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  4. Merge branch 'master' into tor/simple-varinfo-v2

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Commits on Jun 18, 2021

  1. added a couple of convenience constructors

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  2. formatting 

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  3. small fix

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Commits on Jun 20, 2021

  1. return var_info from tilde-statements, allowing impl of immutable ver… 

    …sions
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  2. allow usage of non-Ref types in SimpleVarInfo

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  3. update submodel-macro

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  4. formatting and docstring for submodel-macro

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  5. attempt at supporting implicit returns too

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  6. added a small comment

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  7. simplifed submodel macro a bit

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  8. formatting 

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  9. fixed typo

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  10. Merge branch 'tor/simple-varinfo-v2' of github.com:TuringLang/Dynamic… 

    …PPL.jl into tor/simple-varinfo-v2
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  11. use bang-bang convention

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  12. updated PointwiseLikelihoodContext

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  13. fixed issue where we unnecessarily replace the return-statement

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  14. check subtype in the retval

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  15. formatting

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  16. fixed type-instability in retval check

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  17. introduced evaluate method for model

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  18. remove unnecessary type-requirement

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  19. make return-value check much nicer

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  20. removed redundant creation of anonymous function

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Commits on Jun 28, 2021

  1. dont use UnionAll in return_values

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  2. updated tests for submodel to reflect new syntax

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Commits on Jun 30, 2021

  1. moved to using BangBang-convention for most methods

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  2. remove SimpleVarInfo from this branch

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  3. added a comment

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  4. reverted submodel macro to use = rather than ~

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  5. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  6. updated SimpleVarInfo impl

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  7. added a couple of missing deprecations

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  8. updated tests

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  9. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  10. updated implementations of logjoint and others

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  11. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  12. formatting

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  13. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Jul 2, 2021

  1. added eltype impl for SimpleVarInfo

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  2. formatting

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Commits on Jul 6, 2021

  1. fixed eltype for SimpleVarInfo

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Commits on Jul 9, 2021

  1. implement setindex!! in prep for allowing sampling with immutable vi

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  2. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  3. formatting

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  4. initial work on allowing sampling using SimpleVarInfo

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  5. formatting 

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Commits on Jul 16, 2021

  1. Merge branch 'master' into tor/simple-varinfo-v2

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  2. Merge branch 'tor/simple-varinfo-v2' of github.com:TuringLang/Dynamic… 

    …PPL.jl into tor/simple-varinfo-v2
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  3. add constructor for SimpleVarInfo using model

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  4. improved leftover to_namedtuple_expr, fixing a bug when used with Zygote

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  5. bumped patch version

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  6. Merge branch 'tor/allargs-construction-improvement' into tor/simple-v… 

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Commits on Jul 19, 2021

  1. Merge branch 'master' into tor/simple-varinfo-v2

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  2. Merge branch 'master' into tor/immutable-varinfo-support

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  3. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Jul 20, 2021

  1. fixed set_flag!!

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  2. Merge branch 'master' into tor/immutable-varinfo-support

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  3. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Jul 22, 2021

  1. Merge branch 'master' into tor/immutable-varinfo-support

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  2. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Jul 23, 2021

  1. forgot the return in the replace_returns

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  2. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Jul 29, 2021

  1. Merge branch 'master' into tor/immutable-varinfo-support

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Commits on Aug 2, 2021

  1. bigboy update to benchmarks

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Commits on Aug 5, 2021

  1. fixed some issues and added support for usage of Dict in SimpleVarInfo

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  2. Merge branch 'master' into tor/immutable-varinfo-support

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  3. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  4. added docstring and improved indexing behvaior for SimpleVarInfo

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  5. formatting

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  6. dont allow sampling with indexing when using SimpleVarInfo with Named… 

    …Tuple unless shapes are specified
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Commits on Aug 12, 2021

  1. _setval_kernel and others are only supported by VarInfo atm

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Commits on Aug 14, 2021

  1. Merge branch 'master' into tor/immutable-varinfo-support

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  2. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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  3. fixed typo in comment

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  4. added more values_as impls

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  5. removed redundant values_from_metadata

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Commits on Aug 15, 2021

  1. Merge branch 'master' into tor/immutable-varinfo-support

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  2. Merge branch 'tor/immutable-varinfo-support' into tor/simple-varinfo-v2

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Commits on Aug 17, 2021

  1. fixed bug in push!! for SimpleVarInfo

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Commits on Aug 19, 2021

  1. Merge branch 'master' into tor/benchmark-update

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  2. fixed a couple of bugs in SimpleVarInfo

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  3. forgot which branch Im on

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Commits on Aug 21, 2021

  1. added handling of short defs in replace_returns and more docstrings

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Commits on Aug 23, 2021

  1. fixed bug in generate_tilde introduced in a merge

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  2. fixed a bug in isfuncdef

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  3. fixed tests

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  4. formatting

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Commits on Aug 24, 2021

  1. uncomment mistakenly commented code

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  2. Merge branch 'master' into tor/simple-varinfo-v2

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Commits on Sep 9, 2021

  1. bumped version

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  2. Merge branch 'master' into tor/simple-varinfo-v2

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  3. updated doctests

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  4. dont carry over bang-bang versions that we dont need for general vari… 

    …nfos
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  5. Apply suggestions from @phipsgabler 

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  6. updated tests

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Commits on Nov 3, 2021

  1. Merge branch 'master' into tor/simple-varinfo-v2

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Commits on Nov 6, 2021

  1. removed unnecessary BangBang methods

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  2. fixed zygote rule for dot_observe

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  3. fixed Setfield.jl + returning VarInfo bug in model-macro

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  4. updated tests

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  5. Merge branch 'master' into tor/simple-varinfo-v2

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  6. fixed docs

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  7. formatting

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  8. Merge branch 'master' into tor/simple-varinfo-v2

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  9. fixed issues when using ThreadSafeVarInfo

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Commits on Nov 7, 2021

  1. fixed _pointwise_observe for ThreadSafeVarInfo

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  2. updated ThreadSafeVarInfo

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  3. made SimpleVarInfo compat with ThreadSafeVarInfo and added show

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  4. added some tests for return-values of models

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  5. formatting

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Commits on Nov 8, 2021

  1. fixed doctest for SimpleVarInfo

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  2. formatting

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  3. removed comparison of show from doctest for SimpleVarInfo

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  4. Merge branch 'master' into tor/simple-varinfo-v2

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  5. Update src/compiler.jl 

    Co-authored-by: David Widmann <[email protected]>
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  6. Apply suggestions from code review 

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  7. removed OrderedCollections from docs

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Commits on Nov 9, 2021

  1. some additional fixes

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  2. fixed method ambiguity and some ill-defined map

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Commits on Nov 11, 2021

  1. renamed evaluate to evaluate!!

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Commits on Nov 12, 2021

  1. added implementations of haskey, getindex and setindex!! for SimpleVa… 

    …rInfo
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  2. formatting

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  3. dropped redundant definition

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  4. use getproperty instead of getindex

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  5. fixed method-ambiguity and added some comments

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  6. fixed docstring of SimpleVarInfo

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  7. fixed docstrings

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  8. fixed Project.toml for docs

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  9. fixed docstring of canview

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  10. fixed docstrings

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  11. another attempt at fixing docstrings

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Commits on Nov 17, 2021

  1. added a TODO comment

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  2. remove some output from docstring of SimpleVarInfo

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  3. fixed haskey and hasvalue for AbstractDict

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  4. updated some comments

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  5. updated some errors

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  6. added sampling dot_assume for SimpleVarInfo

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  7. added true versions of density computations to TestUtils

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  8. added tests specific for SimpleVarInfo

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  9. also document TestUtils

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  10. added TestUtils to docs

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  11. fixed setindex!! for SimpleVarInfo using AbstractDict

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  12. added more tests

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  13. formatting

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  14. dont use BangBang for setall!

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  15. revert unnecessary changes to settrans!

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  16. revert unnecessary changes to set_flag!

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  17. revert some changes to docstrings

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  18. fixed some comments and docstrings

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  19. added more convenient logjoint, logprior, and loglikelihood methods

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  20. removed unnecessary export

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  21. fixed export

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    torfjelde committed Nov 17, 2021
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Commits on Nov 20, 2021

  1. use the Setfield impl of getindex, etc. as default and specialize on … 

    …AbstractDict
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    torfjelde committed Nov 20, 2021
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Commits on Nov 22, 2021

  1. fixed docstrings of logjoint, etc.

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    torfjelde committed Nov 22, 2021
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Commits on Nov 23, 2021

  1. Apply suggestions from code review 

    Co-authored-by: Philipp Gabler <[email protected]>
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Commits on Nov 26, 2021

  1. fixed docstring for model

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    torfjelde committed Nov 26, 2021
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  2. replaced return_values by capturing return-value from tilde-statement… 

    …s instead
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    torfjelde committed Nov 26, 2021
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  3. added some tests for return-value of model

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    torfjelde committed Nov 26, 2021
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Commits on Dec 2, 2021

  1. added broadcast_foreach

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    torfjelde committed Dec 2, 2021
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Commits on Dec 6, 2021

  1. Apply suggestions from @devmotion 

    Co-authored-by: David Widmann <[email protected]>
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  2. Merge branch 'tor/simple-varinfo-v2' of github.com:TuringLang/Dynamic… 

    …PPL.jl into tor/simple-varinfo-v2
    @torfjelde
    torfjelde committed Dec 6, 2021
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  3. remove broadcast_foreach for now

    @torfjelde
    torfjelde committed Dec 6, 2021
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  4. some fixes to ThreadSafeVarInfo

    @torfjelde
    torfjelde committed Dec 6, 2021
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  5. Apply suggestions from code review 

    Co-authored-by: David Widmann <[email protected]>
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    torfjelde and devmotion authored Dec 6, 2021
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  6. fixed docstrings

    @torfjelde
    torfjelde committed Dec 6, 2021
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  7. forgot qualification for set

    @torfjelde
    torfjelde committed Dec 6, 2021
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  8. formatting

    @torfjelde
    torfjelde committed Dec 6, 2021
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  9. added comment about why we cant use MacroTools.isdef

    @torfjelde
    torfjelde committed Dec 6, 2021
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  10. remove unnecessary deprecation

    @torfjelde
    torfjelde committed Dec 6, 2021
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  11. udpated some docstrings

    @torfjelde
    torfjelde committed Dec 6, 2021
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  12. fixed more docstrings

    @torfjelde
    torfjelde committed Dec 6, 2021
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  13. make overloads of BangBang methods qualified

    @torfjelde
    torfjelde committed Dec 6, 2021
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  14. remove overloading of values and instead use values_as without the ty… 

    …pe specified
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    torfjelde committed Dec 6, 2021
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  15. Apply suggestions from code review 

    Co-authored-by: David Widmann <[email protected]>
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  16. renamed hasvalue for SimpleVarInfo to _haskey

    @torfjelde
    torfjelde committed Dec 6, 2021
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  17. revert changes from previous commit

    @torfjelde
    torfjelde committed Dec 6, 2021
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Commits on Dec 7, 2021

  1. minor version bump

    @torfjelde
    torfjelde committed Dec 7, 2021
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Commits on Dec 8, 2021

  1. fixed sampling with ThreadSafeVarInfo

    @torfjelde
    torfjelde committed Dec 8, 2021
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  2. fixed setindex!! for ThreadSafeVarInfo

    @torfjelde
    torfjelde committed Dec 8, 2021
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  3. fixed eltype for ThreadSafeVarInfo wrapping a SimpleVarInfo

    @torfjelde
    torfjelde committed Dec 8, 2021
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  4. fixed a test

    @torfjelde
    torfjelde committed Dec 8, 2021
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  5. relax atol in serialization tests a bit

    @torfjelde
    torfjelde committed Dec 8, 2021
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  6. temporarily disable Julia 1.3

    @torfjelde
    torfjelde committed Dec 8, 2021
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  7. relax atol for a prior check

    @torfjelde
    torfjelde committed Dec 8, 2021
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  8. Improvements to @submodel in #309 (#348) 

    * added prefix keyword argument to submodel-macro

* Apply suggestions from code review

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* converted example in docs into test

* fixed docstring

* Apply suggestions from code review

Co-authored-by: Philipp Gabler <[email protected]>

* removed redundant prefix_submodel_context def and added another example to docstring

* fixed doctests

* attempt at fixing doctests

* another attempt at fixing doctests

* had a typo in docstring

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Philipp Gabler <[email protected]>
    @torfjelde @github-actions @phipsgabler
    3 people authored Dec 8, 2021
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Commits on Dec 11, 2021

  1. fixed a test case using submodel

    @torfjelde
    torfjelde committed Dec 11, 2021
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  2. improved docstring according to comments by @devmotion

    @torfjelde
    torfjelde committed Dec 11, 2021
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