Add vignette on how to handle deprecations with $format()

[rok-cesnovar]

Submission Checklist

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

Summary

Adds a vignette on handling deprecations with the canonicalizer available through the $format() method.

Online vignette can be seen here: https://rok-cesnovar.github.io/cmdstanr/articles/deprecations.html

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):
Rok Češnovar

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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.16%. Comparing base (b62ad1f) to head (cc86f4e).
⚠️ Report is 994 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #644      +/-   ##
==========================================
- Coverage   92.63%   91.16%   -1.47%     
==========================================
  Files          12       12              
  Lines        3406     3419      +13     
==========================================
- Hits         3155     3117      -38     
- Misses        251      302      +51     

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[jgabry]

Is there a bug in the format method? I don't think it's actually overwriting the Stan file when overwrite_file=TRUE. If I run

mod$format(
    canonicalize = list("deprecations"),
    overwrite_file = TRUE,
    backup = FALSE
)
mod$print()

Then mod$print() still prints the old version of the file.

[rok-cesnovar]

I think print() might use a stored string of the file?

[jgabry]

Yeah. I think we need to put the string of the new Stan code in private$stan_code_

[jgabry]

Ok I think I fixed the printing issue. If that fix and my edits to the vignette look good to you then I think this is ready.

[jgabry]

Actually I think we also still need to do this part of #626:

catch if any stanc3 message mentions deprecations and print an R warning pointing to the online vignette

[rok-cesnovar]

Actually I think we also still need to do this part of #626:

Yeah, will merge this and then open another PR with the exact link.

Thanks @jgabry for the fixes!