Expand the use of CMDSTAN variable

[rok-cesnovar]

Submission Checklist

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

Summary

Fixes #638

Expands the use of the CMDSTAN environment variable so that if a valid CmdStan installation is not found in the CMDSTAN path, it is used as the top level installation folder (cmdstan installations are a level below).

To test run:

Sys.setenv("CMDSTAN" = "/top/level/folder/of/cmdstan/installs")

library(cmdstanr)

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

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/)

[rok-cesnovar]

@bwiernik when you have a moment, can I ask you to confirm this does what you proposed in #638.

No rush, whenever you get to it. Thanks!

remotes::install_github("stan-dev/cmdstanr@cmdstan-variable-refactor")
Sys.setenv("CMDSTAN" = "/top/level/folder/of/cmdstan/installs")

library(cmdstanr)

[codecov-commenter]

Codecov Report

Merging #643 (394f77f) into master (b62ad1f) will decrease coverage by 1.46%.
The diff coverage is 30.76%.

❗ Current head 394f77f differs from pull request most recent head a3d1d22. Consider uploading reports for the commit a3d1d22 to get more accurate results

@@            Coverage Diff             @@
##           master     #643      +/-   ##
==========================================
- Coverage   92.63%   91.16%   -1.47%     
==========================================
  Files          12       12              
  Lines        3406     3417      +11     
==========================================
- Hits         3155     3115      -40     
- Misses        251      302      +51     

Impacted Files	Coverage Δ
R/zzz.R	64.15% <20.00%> (-10.85%)	⬇️
R/path.R	79.03% <66.66%> (-0.97%)	⬇️
R/install.R	58.35% <0.00%> (-8.52%)	⬇️
R/utils.R	89.63% <0.00%> (-1.04%)	⬇️
R/csv.R	97.78% <0.00%> (-0.89%)	⬇️
R/model.R	91.33% <0.00%> (-0.76%)	⬇️
R/run.R	95.23% <0.00%> (-0.50%)	⬇️

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[bwiernik]

I tried it out. It seems to be working, but there is still an unnecessary warning when the environment variable is set to a higher-level directory:

> Sys.setenv("CMDSTAN" = "~/cmdstanr")
> library(cmdstanr)
CmdStan path set to: /Users/brenton/cmdstanr/cmdstan-2.29.2
This is cmdstanr version 0.5.1
- CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
- CmdStan path: /Users/brenton/cmdstanr/cmdstan-2.29.2
- CmdStan version: 2.29.2
Warning message:
Can't find CmdStan makefile to detect version number. Path may not point to valid installation. 

[rok-cesnovar]

Ah, that was sloppy testing on my end. Thanks @bwiernik for testing! I think this should now be fixed.

In case that no installation is found but the env. variable is set, it will display a warning:

No CmdStan installation found in the path specified by the environment variable 'CMDSTAN'.

[jgabry]

Looks good!