Global option for turning off warning for partial initial values

[jgabry]

closes #912

Submission Checklist

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

Summary

Adds a global option to turn off warning about partial initial value specification. When options(cmdstanr_warn_inits=TRUE) (the default) the warning message now looks like this, with a new line about disabling the warning:

Init values were only set for a subset of parameters. 
Missing init values for the following parameters:
alpha, beta

To disable this message use options(cmdstanr_warn_inits = FALSE).

When options(cmdstanr_warn_inits=FALSE) there is now no message at all.

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):
Columbia University

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]

@ben18785 I think this should give you what you were asking for in #912. Do you want to test this out before we merge it?

[jgabry]

Looks like the Windows failures are due to issues in the install_cmdstan step when it tries to run pacman:

Error in `processx::run("pacman", args = c("-Sy", install_pkgs, "--noconfirm"), …`:
16
! System command 'pacman' failed

https://github.com/stan-dev/cmdstanr/actions/runs/7732239038/job/21081730518?pr=913#step:11:16

[ben18785]

Thanks very much @jgabry -- works perfectly as described above.

[jgabry]

Thanks very much @jgabry -- works perfectly as described above.

Great, thanks for testing.

[jgabry]

Looks like the Windows failures are due to issues in the install_cmdstan step when it tries to run pacman:

Error in `processx::run("pacman", args = c("-Sy", install_pkgs, "--noconfirm"), …`:
16
! System command 'pacman' failed

https://github.com/stan-dev/cmdstanr/actions/runs/7732239038/job/21081730518?pr=913#step:11:16

@rok-cesnovar Any idea if this Windows issue is something we need to fix or just some temporary issue that will resolve itself (as is often the case with GitHub actions)?

[jgabry]

@rok-cesnovar Any idea if this Windows issue is something we need to fix or just some temporary issue that will resolve itself (as is often the case with GitHub actions)?

Looks like this pacman issue is affecting users too: https://twitter.com/fusaroli/status/1753094135513493693

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.32%. Comparing base (4b94b11) to head (3c678d1).

❗ Current head 3c678d1 differs from pull request most recent head 6bf9b3d. Consider uploading reports for the commit 6bf9b3d to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #913   +/-   ##
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  Coverage   88.32%   88.32%           
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  Files          12       12           
  Lines        4548     4549    +1     
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+ Hits         4017     4018    +1     
  Misses        531      531           

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[jgabry]

Finally got everything passing here. I think this is a small enough change I could just merge, but will leave open for a bit longer in case @rok-cesnovar or @andrjohns has any issue with this.

[rok-cesnovar]

Looks great!

[jgabry]

Ok cool will go ahead and merge