add generate_quantities timing support

[avehtari]

Closes #1070 after the next CmdStan release.

CmdStan develop version adds now timing information to standalone generated quantities csv. This PR adds CmdStanR support so that the timing reporting with $generate_quantities() matches $sample().

For CmdStan 2.38 and earlier the timing reported stays the same, that is, showing 0.0 seconds.

Example output with CmdStan 2.39+

Running standalone generated quantities after 4 MCMC chains, all chains in parallel ...

Chain 3 finished in 1.3 seconds.
Chain 4 finished in 1.4 seconds.
Chain 2 finished in 1.7 seconds.
Chain 1 finished in 1.9 seconds.

All 4 chains finished successfully.
Mean chain execution time: 1.6 seconds.
Total execution time: 2.0 seconds.

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/)

[jgabry]

Thanks Aki. Looks like some tests are failing.

[avehtari]

Some tests may fail if not using the develop version of CmdStan. I only thought that the actual code would work with old CmdStan, but did not think that it would be easier if the tests also work with old versions. Will fix tomorrow

[avehtari]

Can we have conditional tests based on the CmdStan version? I tried to look at examples in tests, but didn't find a clear example

[jgabry]

Can we have conditional tests based on the CmdStan version? I tried to look at examples in tests, but didn't find a clear example

We used to have a lot of tests like this for older versions of CmdStan but they were removed recently because for v1.0 we will require at least CmdStan v2.35.0. You can do things like this:

if (cmdstan_version() >= "2.39.0") {
  expect_true(...)
} 

But if the development version of CmdStan is not installed on any of the GitHub actions runs then the new functionality won't actually be tested. We could either setup one of the CI runs to use the development version so we can test it now or we could wait to merge this until the next CmdStan release.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.75000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.46%. Comparing base (24acf13) to head (9f9f877).

Files with missing lines	Patch %	Lines
R/csv.R	95.83%	1 Missing ⚠️
R/run.R	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1168      +/-   ##
==========================================
+ Coverage   90.57%   91.46%   +0.88%     
==========================================
  Files          15       15              
  Lines        6131     6149      +18     
==========================================
+ Hits         5553     5624      +71     
+ Misses        578      525      -53     

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[jgabry]

Now that CmdStan 2.39 was released we can go ahead with this. I found a couple of small issues, but I'll make some commits soon and then we can merge.

[jgabry]

Ok I made a few changes and we can merge when all the checks pass