Fix model$format and model$check_syntax for compiled models with include-paths

[adrian-lison]

Submission Checklist

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

Summary

This PR fixes #774 by using self$include_paths() instead of private$precompile_include_paths_ in the methods check_syntax and format. This is because the latter only holds the include_paths if the model has not been compiled yet. As a result, it is now possible to call these methods on compiled models with include statements without getting a syntax error from stanc. For format, this has currently not been possible at all, for check_syntax, you always had to use the include_paths argument of the function even if the same, default include_paths were used.

The PR also adds tests for include_paths in check_syntax and format on compiled models, but I am not sure if these are desired as they require compilation of the example model during testing.

This is my first PR for cmdstanr, so apologies in case I violated any conventions.

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):
Adrian Lison

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/)

[rok-cesnovar]

Thanks so much @adrian-lison! This looks great.

[andrjohns]

The json failures in the CI here are due to the jsonlite package (opened issue here).

As only the json tests failed and all other passed, I'll merge this

[jgabry]

Thanks for fixing this!

…

On Fri, Jun 23, 2023 at 10:06 AM Andrew Johnson ***@***.***> wrote: Merged #775 <#775> into master. — Reply to this email directly, view it on GitHub <#775 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3PQQ2YYTSDSMFQVCQCFFLXMW5IFANCNFSM6AAAAAAZQCJNP4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>