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Remove dep on DynamicPPL in package extentions #226

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merged 4 commits into from
Oct 24, 2024

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@sunxd3 sunxd3 commented Oct 23, 2024

This PR remove further dependency of DynamicPPL in package extensions.

  • in MCMCChains extension, varname_leaves util function is copied from DynamicPPL
  • DynamicPPL extension used to have a single function that produce a DynamicPPL compatible SimpleVarInfo. This is still supported, only now the function is moved into the main package and produce a OrderDict{<:VarName, }, so when we make the integration, a single SimpleVarInfo(ordered_dict) would work.

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github-actions bot commented Oct 23, 2024

BridgeStan not found at location specified by $BRIDGESTAN environment variable, downloading version 2.5.0 to /home/runner/.bridgestan/bridgestan-2.5.0
Done!
Model dogs produces error: ErrorException("log_density() failed with exception: Exception: bernoulli_lpmf: Probability parameter is inf, but must be in the interval [0, 1] (in '/home/runner/work/JuliaBUGS.jl/JuliaBUGS.jl/benchmark/stan/bugs_examples/vol1/dogs/dogs.stan', line 37, column 6 to line 38, column 62)\n")

Model Parameter Count Data Count Stan Density Time (µs) Stan Density Gradient Time (µs) JuliaBUGS Density Time with Graph Walk (µs) JuliaBUGS Density Gradient Time with ReverseDiff.jl(compiled tape) (µs)
rats 65 150 5.6326 8.21867 6977.95 101.47
pumps 12 10 1.00462 1.39309 176.32 6.745
dogs 2 720 NA NA 3550.27 151.353
seeds 26 21 2.47827 3.15583 701.39 20.839
surgical_realistic 14 12 1.24025 1.70317 236.653 9.01367
magnesium 108 96 10.6195 12.5385 9274.57 80.851
salm 22 18 2.58936 3.255 494.894 13.866
equiv 15 20 2.53482 3.45138 368.177 17.853
dyes 9 30 1.01475 1.38067 242.462 13.405
stacks 6 21 1.13904 1.74794 325.168 14.878
epil 303 236 33.012 39.714 64558.0 283.85
blockers 47 44 3.28389 3.76129 2020.17 31.159
oxford 244 240 16.14 18.916 48133.6 194.303
lsat 1006 5000 181.048 222.845 2.99378e6 3975.85
bones 33 422 72.766 92.943 14504.9 199.232
mice 20 65 7.33625 9.36733 1031.13 40.235
kidney 64 58 10.7 16.29 3698.82 76.413
leuk 18 714 20.437 26.81 9723.04 207.077
leukfr 40 714 24.045 31.809 18609.9 255.185

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Pull Request Test Coverage Report for Build 11487515514

Details

  • 1 of 21 (4.76%) changed or added relevant lines in 2 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage decreased (-0.3%) to 77.678%

Changes Missing Coverage Covered Lines Changed/Added Lines %
ext/JuliaBUGSMCMCChainsExt.jl 1 10 10.0%
src/model.jl 0 11 0.0%
Totals Coverage Status
Change from base Build 11433118017: -0.3%
Covered Lines: 1378
Relevant Lines: 1774

💛 - Coveralls

@sunxd3 sunxd3 merged commit 53e9de6 into master Oct 24, 2024
12 of 13 checks passed
@sunxd3 sunxd3 deleted the sunxd/remove_dynamicppl_complete branch October 24, 2024 06:49
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2 participants