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Fix DistributionLogPotential interface + add test using mRNA transfection model #221
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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 |
windows issues with stan, weird https://github.com/Julia-Tempering/Pigeons.jl/actions/runs/8636249839/job/23675680859#step:8:1352 |
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: |
Ok so apparently this is a major regression on Julia 1.10 in Windows. Weird that we just experienced this here though...? |
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 |
Codecov ReportAttention: Patch coverage is
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #221 +/- ##
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- Coverage 86.82% 83.10% -3.72%
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Files 95 95
Lines 2429 2427 -2
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- Hits 2109 2017 -92
- Misses 320 410 +90 ☔ View full report in Codecov by Sentry. |
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) .