Update handling of show_messages, add show_exceptions

[andrjohns]

Submission Checklist

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

Summary

This PR addresses #718 and #646 by adding a show_exceptions argument to the sample() and sample_mpi() methods, and also expands the use of show_messages=FALSE to completely suppress all printing of non-errors.

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/)

[andrjohns]

This PR is technically changing user-facing behaviour, so it should probably get signed off by both @jgabry and @rok-cesnovar.

The current value of show_messages is used for both stdout and stderr handling. This PR changes this to have show_exceptions refer to stderr behaviour and show_messages refer to stdout.

Is that alright with both of you or should we keep it as a single show_messages argument (but with the expansions to suppress more output)?

[codecov-commenter]

Codecov Report

Merging #746 (5440f47) into master (4c4dd09) will decrease coverage by 0.01%.
The diff coverage is 90.90%.

❗ Current head 5440f47 differs from pull request most recent head d24a359. Consider uploading reports for the commit d24a359 to get more accurate results

@@            Coverage Diff             @@
##           master     #746      +/-   ##
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- Coverage   86.20%   86.20%   -0.01%     
==========================================
  Files          12       12              
  Lines        4082     4095      +13     
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+ Hits         3519     3530      +11     
- Misses        563      565       +2     

Impacted Files	Coverage Δ
R/run.R	93.73% <88.88%> (-0.21%)	⬇️
R/model.R	90.43% <100.00%> (+0.02%)	⬆️

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[rok-cesnovar]

I like this. It does change user-facing outputs, but I think the current show_messages was not doing everything it should have been, so most users were using suppress... R functions anyways in cases where show_messages would have been applicable.

[jgabry]

I like this. It does change user-facing outputs, but I think the current show_messages was not doing everything it should have been, so most users were using suppress... R functions anyways in cases where show_messages would have been applicable.

Agree!