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Remove dependency on DynamicPPL #221

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merged 12 commits into from
Oct 10, 2024
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@sunxd3 sunxd3 commented Oct 7, 2024

fix #206

@sunxd3 sunxd3 marked this pull request as draft October 7, 2024 08:13
sunxd3 and others added 5 commits October 7, 2024 16:15
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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github-actions bot commented Oct 7, 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-example-models/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 5.5084 8.142 7208.56 92.612
pumps 12 10 1.00876 1.44219 184.294 6.71975
dogs 2 720 NA NA 3920.58 161.972
seeds 26 21 2.44542 3.20094 689.059 21.781
surgical_realistic 14 12 1.28852 1.72403 240.247 9.00333
magnesium 108 96 10.475 12.1875 9727.02 90.218
salm 22 18 2.37345 3.07911 507.1 13.2245
equiv 15 20 2.47555 3.44763 379.157 15.819
dyes 9 30 0.980167 1.32382 252.701 13.6055
stacks 6 21 1.14215 1.67589 309.257 14.937
epil 303 236 33.472 38.873 68533.9 324.13
blockers 47 44 3.30625 3.76414 2120.03 32.751
oxford 244 240 16.14 18.735 54958.3 202.888
lsat 1006 5000 181.459 222.826 3.15041e6 1645.79
bones 33 422 72.605 91.1 14576.4 195.585
mice 20 65 7.3385 9.25067 1075.1 43.902
kidney 64 58 10.64 16.15 3824.87 78.296
leuk 18 714 20.438 26.87 9715.78 243.454
leukfr 40 714 24.255 31.87 19139.3 253.137

sunxd3 and others added 5 commits October 7, 2024 11:12
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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coveralls commented Oct 10, 2024

Pull Request Test Coverage Report for Build 11271788411

Details

  • 105 of 147 (71.43%) changed or added relevant lines in 10 files are covered.
  • 57 unchanged lines in 5 files lost coverage.
  • Overall coverage decreased (-3.5%) to 77.929%

Changes Missing Coverage Covered Lines Changed/Added Lines %
ext/JuliaBUGSAdvancedMHExt.jl 0 3 0.0%
src/model.jl 54 62 87.1%
ext/JuliaBUGSDynamicPPLExt.jl 0 14 0.0%
src/utils.jl 9 26 34.62%
Files with Coverage Reduction New Missed Lines %
src/parser/bugs_macro.jl 1 76.85%
ext/JuliaBUGSAdvancedMHExt.jl 1 28.57%
src/compiler_pass.jl 6 93.94%
src/model.jl 8 83.66%
src/BUGSExamples/BUGSExamples.jl 41 0.0%
Totals Coverage Status
Change from base Build 11210106726: -3.5%
Covered Lines: 1377
Relevant Lines: 1767

💛 - Coveralls

@sunxd3 sunxd3 marked this pull request as ready for review October 10, 2024 12:36
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sunxd3 commented Oct 10, 2024

@yebai I am merging this now, there might be corner cases DynamicPPL handles and I have not integrated yet, will fix those as we go

@sunxd3 sunxd3 merged commit 4689df3 into master Oct 10, 2024
12 of 13 checks passed
@sunxd3 sunxd3 deleted the sunxd/start_striping_dynamicppl branch October 10, 2024 12:37
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Remove dependency on DynamicPPL.
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