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Compatibility fixes for cmdstan 2.33+ #843

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merged 11 commits into from Sep 13, 2023
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@jgabry jgabry commented Sep 6, 2023

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  • Run unit tests
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Summary

Fixes old array syntax in some examples.
I've been teaching a Stan workshop and noticed when showing the cmdstanr doc that we still use the old array syntax in a few places.

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Columbia University

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@jgabry jgabry marked this pull request as ready for review September 6, 2023 21:41
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jgabry commented Sep 6, 2023

I think there’s something else in the deprecations vignette that’s causing an error but I don’t have time to check right now. Will come back to this later tonight or in the next few days.

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jgabry commented Sep 7, 2023

@rok-cesnovar @andrjohns Actually the Deprecations vignette is now just wrong because it's all about deprecation warnings but all the warnings it shows are now errors as of 2.33. So we need to decide what to do about that vignette. Do we want to rewrite it to be about fixing errors instead of warnings? Something else? Until we figure that out every cmdstanr PR will error during unit tests because this vignette won't run with 2.33

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jgabry commented Sep 7, 2023

@rok-cesnovar @andrjohns Actually the Deprecations vignette is now just wrong because it's all about deprecation warnings but all the warnings it shows are now errors as of 2.33. So we need to decide what to do about that vignette. Do we want to rewrite it to be about fixing errors instead of warnings? Something else? Until we figure that out every cmdstanr PR will error during unit tests because this vignette won't run with 2.33

I pushed one commit yesterday that I thought would fix it (changing array syntax) but turns out all the other warnings are errors now too. So not sure what we want to do about that.

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I would remove it and make an issue to make a short vignette on how to use the auto-formatter to convert these models.

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jgabry commented Sep 7, 2023

That sounds good to me

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jgabry commented Sep 7, 2023

This is still failing after removing the vignette, apparently because 2.33 broke a few things in cmdstanr. E.g., expose_functions seems to be broken (see #845). So I don't think I can get the tests to pass until we fix that.

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I'm going to merge #847 into this PR/branch since the vignette deprecations are also causing the tests in that PR to fail.

Then we can make this PR a general 2.33-fixes PR if anything else pops up

@andrjohns andrjohns mentioned this pull request Sep 11, 2023
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@andrjohns andrjohns changed the title update old array syntax in some examples Compatibility fixes for cmdstan 2.33+ Sep 11, 2023
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jgabry commented Sep 11, 2023

Sounds good, thanks @andrjohns!

@jgabry jgabry mentioned this pull request Sep 11, 2023
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Codecov Report

Merging #843 (869e7a8) into master (5e2551c) will decrease coverage by 1.97%.
The diff coverage is 92.30%.

❗ Current head 869e7a8 differs from pull request most recent head 1caa732. Consider uploading reports for the commit 1caa732 to get more accurate results

@@            Coverage Diff             @@
##           master     #843      +/-   ##
==========================================
- Coverage   88.38%   86.41%   -1.97%     
==========================================
  Files          12       12              
  Lines        4201     4212      +11     
==========================================
- Hits         3713     3640      -73     
- Misses        488      572      +84     
Files Changed Coverage Δ
R/example.R 97.56% <ø> (ø)
R/fit.R 96.22% <ø> (ø)
R/model.R 91.25% <ø> (+0.13%) ⬆️
R/utils.R 70.56% <92.30%> (-3.94%) ⬇️

... and 3 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

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@jgabry @rok-cesnovar this is passing and ready to have a look at. The only change that I'm not sure about is that reading estimates after a failed $optimize() run is now erroring when it doesn't under 2.32

No idea why, or how important it is

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The changes look good. I dont know about the optimize(), will investigate whether this was a change in cmdstan, but I think we can merge the PR before that.

@andrjohns andrjohns merged commit b29374e into master Sep 13, 2023
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@andrjohns andrjohns deleted the fix-old-array-syntax branch September 13, 2023 09:18
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jgabry commented Sep 13, 2023

Looks good to me too, thanks!

@jgabry jgabry linked an issue Sep 13, 2023 that may be closed by this pull request
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expose_functions errors after update to 2.33
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