Remove duplicate acceptance procedure, update tests

[betanalpha]

Submisison Checklist

• Run unit tests: ./runTests.py src/test/unit
• Run cpplint: make cpplint
• Declare copyright holder and open-source license: see below

Summary

Removes duplicate acceptance procedure in the default NUTS algorithm that was causing chains to push too far out into the tails.

Intended Effect

Restores correctness of default NUTS algorithm.

How to Verify

The following model,

parameters {
  real<lower=0, upper=1> x;
}
model {
  x ~ uniform(0, 1);
}

should now return an actually uniform distribution.

Side Effects

Small changes to all default sampler output.

Documentation

None.

Reviewer Suggestions

@syclik, @bob-carpenter, @bgoodri

Copyright and Licensing

Copyright: University of Warwick.

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/)

[betanalpha]

No idea what's going on with Travis -- and where is Jenkins?

[syclik]

Code looks good. Just verified it fixes the model in question.

[betanalpha]

Yeah, it’ll fix the uniform model and the model Ben has introduced a few
weeks ago. The logistic test will fail, however, so I need Jenkins to run
to get the Windows-specific values to update the hard-coded values.

On Jul 26, 2016, at 2:48 PM, Daniel Lee notifications@github.com wrote:

Code looks good. Just verified it fixes the model in question.

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[syclik]

Those values are on Mac OS X, so you should be able to run locally.

[betanalpha]

They’ve never translated before — the values I get locally would
be very slightly off from what Jenkins reported. Has that test moved
to an OS X recently?

On Jul 26, 2016, at 3:05 PM, Daniel Lee notifications@github.com wrote:

Those values are on Mac OS X, so you should be able to run locally.

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[syclik]

Nope. They've always been Mac OS X tests.

On Tue, Jul 26, 2016 at 10:08 AM, Michael Betancourt <
notifications@github.com> wrote:

They’ve never translated before — the values I get locally would
be very slightly off from what Jenkins reported. Has that test moved
to an OS X recently?

On Jul 26, 2016, at 3:05 PM, Daniel Lee notifications@github.com wrote:

Those values are on Mac OS X, so you should be able to run locally.

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