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Fix DistributionLogPotential interface + add test using mRNA transfection model #221

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merged 7 commits into from
Apr 11, 2024

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miguelbiron
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@miguelbiron miguelbiron commented Apr 10, 2024

Target for test is written in stan with iid sampling enabled by a DistributionLogPotential. It is built so that if rounds are increased enough, it should recreate Fig. 6 in Ballnus et al. (2017) .

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Got a deprecation msg cc @alexandrebouchard

┌ Warning: StanModel(;stan_file,... ) is deprecated. Use the normal constructor, StanModel(...) instead.
│   caller = StanLogPotential(stan_file::String, data::String, extra_information::Nothing) at interface.jl:9
└ @ PigeonsBridgeStanExt ~/work/Pigeons.jl/Pigeons.jl/ext/PigeonsBridgeStanExt/interface.jl:9

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Issue persists after rerun. Weird that it only occurs on julia 1.10 -- the test on windows under julia 1.9 works fine. Raised an issue at bridgestan's repo:

roualdes/bridgestan#226

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Ok so apparently this is a major regression on Julia 1.10 in Windows. Weird that we just experienced this here though...?

JuliaLang/julia#52272

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Huh so it looks like we weren't running any stan examples on windows, so of course all tests passed. For example, compare searching for 'bridgestan' in the logs on a windows run -- which gives 4 hits -- to an ubuntu run -- throws 100 hits.

I'm gonna follow this practice and just wrap the stan test in !is_windows_in_CI to close this issue.

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Codecov Report

Attention: Patch coverage is 40.00000% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 83.10%. Comparing base (ab190b8) to head (9ca6cd5).

Files Patch % Lines
ext/PigeonsBridgeStanExt/interface.jl 0.00% 3 Missing ⚠️

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Additional details and impacted files
@@            Coverage Diff             @@
##             main     #221      +/-   ##
==========================================
- Coverage   86.82%   83.10%   -3.72%     
==========================================
  Files          95       95              
  Lines        2429     2427       -2     
==========================================
- Hits         2109     2017      -92     
- Misses        320      410      +90     

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@miguelbiron miguelbiron merged commit 1d4e0bc into main Apr 11, 2024
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@miguelbiron miguelbiron deleted the try-mrna branch April 11, 2024 01:08
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2 participants