verbose mode and replace regexpr

[rok-cesnovar]

Summary

Fixes #385
Fixes #391

I was in a slam dunk issue squashing mood so decided to squash these two.

Copyright and Licensing

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Rok Češnovar

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• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)

[jgabry]

I was in a slam dunk issue squashing mood so decided to squash these two.

Nice, thanks!

This looks great except that the uses of is_verbose_mode all need to be is_verbose_mode() so that it actually calls the function. That's probably why there are errors. I can go ahead and make that change now.

[jgabry]

The way you had this function was totally fine, but to simplify things I changed it to use getOption(), which conveniently handles the NULL case with the default argument.

[rok-cesnovar]

Ah didnt know that. Thanks!

[jgabry]

Ok I changed is_verbose_mode to is_verbose_mode() so we'll see if all the tests pass now. We should also think about where to document that verbose mode is available. It's not really intended for regular users but we should probably mention it briefly somewhere.

[codecov-io]

Codecov Report

Merging #392 (d59e446) into master (775d1e6) will decrease coverage by 0.15%.
The diff coverage is 89.58%.

@@            Coverage Diff             @@
##           master     #392      +/-   ##
==========================================
- Coverage   88.20%   88.05%   -0.16%     
==========================================
  Files          12       12              
  Lines        2713     2720       +7     
==========================================
+ Hits         2393     2395       +2     
- Misses        320      325       +5     

Impacted Files	Coverage Δ
R/install.R	51.64% <50.00%> (-0.32%)	⬇️
R/model.R	80.62% <100.00%> (+0.09%)	⬆️
R/read_csv.R	98.78% <100.00%> (ø)
R/run.R	95.06% <100.00%> (-0.54%)	⬇️
R/utils.R	93.54% <100.00%> (+0.04%)	⬆️

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[rok-cesnovar]

Maybe we add it to the internals vignette? Do we want to do it here or add to the vignette list?

[jgabry]

Maybe we add it to the internals vignette? Do we want to do it here or add to the vignette list?

Sounds good. Either way is fine by me.

[rok-cesnovar]

Will add it here tomorrow and then merge.

[jgabry]

Ok cool, thanks!

[rok-cesnovar]

@jgabry I updated the vignette, check whenever you have a few moments.

[jgabry]

Looks great! I'm going to quickly add an example to the section you created so people can see what the verbose mode output looks like and then I'll merge this.