add show_messages and show_exceptions to generate_quantities

[avehtari]

Summary

Closes #1140. generate_quantities was missing arguments show_messages and show_exceptions. This PR adds them, and also adds tests.

• R/model.R — generate_quantities() method
  • Added show_messages = TRUE and show_exceptions = TRUE to the function signature
  • Passed them to CmdStanGQProcs$new() as show_stdout_messages = show_messages and show_stderr_messages = show_exceptions
• tests/testthat/test-model-generate_quantities.R and
  • Added test: "no output with show_messages = FALSE"
• tests/testthat/test-model-pathfinder.R
  • Added test: "no output with show_messages = FALSE" (pathfinder already had the arguments implemented, just lacked a test)

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):

Aki Vehtari

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 87.51%. Comparing base (453084b) to head (43270b5).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1142      +/-   ##
==========================================
+ Coverage   87.49%   87.51%   +0.01%     
==========================================
  Files          14       14              
  Lines        5983     5982       -1     
==========================================
  Hits         5235     5235              
+ Misses        748      747       -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[avehtari]

I updated the summary with more details

[jgabry]

Thanks, this looks good.