Expose skeleton

[andrjohns]

Submission Checklist

• Run unit tests
• Declare copyright holder and agree to license (see below)

Summary

Packages like https://github.com/n-kall/priorsense and https://github.com/stan-dev/loo will need access to the parameter skeleton from the constrain_pars function for full compatibility with cmdstanr.

This PR adds a boolean flag to the constrain_pars method to return only the parameter skeleton rather than the constrained pars:

> fit$constrain_pars(skeleton_only = TRUE)
$theta
[1] 0

$log_lik
 [1] 0 0 0 0 0 0 0 0 0 0

As part of this, the model_variables object is updated to include the parameter sizes from the model when the model methods are initialised.

Copyright and Licensing

Please list the copyright holder for the work you are submitting
(this will be you or your assignee, such as a university or company):
Andrew Johnson

By submitting this pull request, the copyright holder is agreeing to
license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[codecov-commenter]

Codecov Report

Merging #706 (f979f2a) into master (39a5c4c) will decrease coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #706      +/-   ##
==========================================
- Coverage   90.56%   90.53%   -0.03%     
==========================================
  Files          12       12              
  Lines        3888     3890       +2     
==========================================
+ Hits         3521     3522       +1     
- Misses        367      368       +1     

Impacted Files	Coverage Δ
R/fit.R	98.17% <100.00%> (+<0.01%)	⬆️
R/install.R	62.70% <0.00%> (-0.24%)	⬇️

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

[andrjohns]

@rok-cesnovar I realised I'd made a bunch of redundant/unnecessary changes with the PR, so I've reverted those. Makes for a much simpler diff ha!

[rok-cesnovar]

Love it!

[jgabry]

Awesome, thanks!

…

On Thu, Oct 20, 2022 at 3:49 AM Rok Češnovar ***@***.***> wrote: Merged #706 <#706> into master. — Reply to this email directly, view it on GitHub <#706 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3PQQ7FZO3QZCTK27UXBWTWED2PRANCNFSM6AAAAAARGZF5HE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jgabry]

Awesome, thanks!