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Reduce dependence on cmdstanr given it's suggested not required #362

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athowes opened this issue Oct 2, 2024 · 1 comment · Fixed by #424
Closed

Reduce dependence on cmdstanr given it's suggested not required #362

athowes opened this issue Oct 2, 2024 · 1 comment · Fixed by #424
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athowes commented Oct 2, 2024

I think make a new issue for handling this with my preference being to stop being opinionated about the backend in the core package. We can talk about doing so (and how to) in the vignettes. The minimal version is we use rstan everywhere and put a comment about preferring cmdstanr in the FAQ

Originally posted by @seabbs in #356 (comment)
@athowes athowes added the high Required for next release label Oct 2, 2024
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athowes commented Oct 2, 2024 •
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This plan seems fine to me.

When I've previously tried to migrate to rstan in tests it has thrown fails. So that will probably have to be tackled if we want to move to using rstan in tests.

@athowes athowes mentioned this issue Nov 6, 2024
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@athowes athowes linked a pull request Nov 7, 2024 that will close this issue
Issue #362: Reduce dependence on cmdstanr #424
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@athowes athowes self-assigned this Nov 13, 2024
seabbs added a commit that referenced this issue Nov 14, 2024
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
4afb056 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
@athowes athowes mentioned this issue Nov 14, 2024
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Issue #362: Reduce dependence on cmdstanr epinowcast/epidist
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