use CSV/stdout reported time for time()

[rok-cesnovar]

Submission Checklist

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

Summary

Fixes #303

> fit$time()
$total
[1] 0.9245193

$chains
  chain_id warmup sampling total
1        1  0.026    0.375 0.401
2        2  0.017    0.417 0.434
3        3  0.017    0.383 0.400
4        4  0.018    0.398 0.416

which matches the CSV reported times.

For fixed_param

> fit$time()
$total
[1] 0.1305542

$chains
  chain_id warmup sampling total
1        1      0    0.111 0.111

warmup is 0, which is correct as @yizhang-yiz points out.

$time()$total is still the Sys.time()-timed execution time. That is the time to execute all chains and will differ depending on how many chains you run in parallel. Non-sampling methods do not have time reports in the CSV or stdout so those still use Sys.time() as well.

$time()$chains reports times reported in stdout (CSV).

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, Univ. of Ljubljana

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)

[codecov-commenter]

Codecov Report

Merging #307 into master will decrease coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #307      +/-   ##
==========================================
- Coverage   90.15%   90.12%   -0.03%     
==========================================
  Files          12       12              
  Lines        2428     2421       -7     
==========================================
- Hits         2189     2182       -7     
  Misses        239      239              

Impacted Files	Coverage Δ
R/run.R	97.08% <100.00%> (-0.05%)	⬇️

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[rok-cesnovar]

Will add a simple test just for sanity check that CSV times match but otherwise this is ready for review.