Feature/659 diagnose verbose

[mitzimorris]

Submisison Checklist

• Run tests: ./runCmdStanTests.py src/test
• Declare copyright holder and open-source license: see below

Summary:

Added output stmts for:

• names of csv files parsed
• msgs for each diagnostic; if diagnostic is OK, outputs "satisfactory" message.
• processing completed

Intended Effect:

Always provide output for command - if diagnose command doesn't find problems, then it will print the following message:

Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory for all transitions.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

How to Verify:

unit tests

Side Effects:

none.

Documentation:

updated cmdstan user's guide accordingly

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/)

[syclik]

@mitzimorris, some basic things:

1. who owns the copyright?
2. could you please update the issue (or the PR) to say what this does? I had to fire up everything to figure out that the output looks like:

Processing csv files: 1.csv, 2.csv, 3.csv, 4.csv, 5.csv

All transitions within treedepth limit.

No divergent transitions.

Processing complete.

3. There are no line breaks in the message if there's a divergence? This just looks weird.
4. Did you want a summary in the processing complete line? Or at least an "exiting with error" or something?

[mitzimorris]

made requested changes to program output.
updated PR description - added example output for model which passes all diagnostics, assigned copyright to Columbia University.

[bob-carpenter]

I'd prefer this to be set up so that each test provides a warning/error or an "all's well" output.

Then the has_errors flag isn't necessary and the "all's well" messages can just be moved up as else conditions on the relevant tests. The doc would need to change a bit, too.

[bob-carpenter]

For some reason, I didn't see that @syclik had already started reviewing this. So take my input as an optional suggestion. I just approved my change request so it won't block anything.

[mitzimorris]

@syclik - done making changes - please review.

discussed Rhat msg with Ben and Aki at today's Stan meeting. using constant to allow for future changes.

[mitzimorris]

@syclik - are messages OK?

[syclik]

Thanks!

[syclik]

Sorry--I missed the original notification. Please feel free to ping me again if that happens.

It's approved.

[mitzimorris]

@syclik - thanks!