Inline functions

[rgiordan]

Submisison Checklist

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

Summary:

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)

[stan-buildbot]

Can one of the admins verify this patch?

[syclik]

Jenkins, ok to test.

[betanalpha]

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[rgiordan]

I actually have no idea. Formally, I am a "visiting scholar" at Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[betanalpha]

I think it would be prudent — any relevant issues on the Columbia side
would be in any documents you signed. We had to go through significant
red tape to get the open source okay from Columbia and I don’t think it’s
blanket to any contribution to Stan, but perhaps someone can comment?
No idea if it’s any easier from the Berkeley side.

On Jul 7, 2016, at 10:56 PM, Ryan notifications@github.com wrote:

I actually have no idea. Formally, I am a "visiting scholar" at Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[rgiordan]

Fair enough. I've sent an email to the Berkeley research group that I'm
part of. Hopefully someone has some experience with this.

On Thu, Jul 7, 2016 at 5:00 PM, Michael Betancourt <notifications@github.com

wrote:

I think it would be prudent — any relevant issues on the Columbia side
would be in any documents you signed. We had to go through significant
red tape to get the open source okay from Columbia and I don’t think it’s
blanket to any contribution to Stan, but perhaps someone can comment?
No idea if it’s any easier from the Berkeley side.

On Jul 7, 2016, at 10:56 PM, Ryan notifications@github.com wrote:

I actually have no idea. Formally, I am a "visiting scholar" at Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <
notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[bob-carpenter]

Yes, it's blanket to any contribution to Stan now and in the future.

Berkeley's very liberal about allowing open-source. They're the
"B" in "BSD", after all. They're also the ones behind AmpLab.

Most universities seem to be OK with open source, though they
often ask you to verify. Columbia Tech Ventures in the end was surprised
we were asking them because they say they always allow researchers to release
things open source if that's what they want to do. We could've saved
ourselves a lot of time had we gone to the top earlier.

And no university is going to think it needs to preserve rights to
patches to other software---there's nothing for them to gain from it.
It's the money trail, as usual.

• Bob

On Jul 7, 2016, at 5:00 PM, Michael Betancourt notifications@github.com wrote:

I think it would be prudent — any relevant issues on the Columbia side
would be in any documents you signed. We had to go through significant
red tape to get the open source okay from Columbia and I don’t think it’s
blanket to any contribution to Stan, but perhaps someone can comment?
No idea if it’s any easier from the Berkeley side.

On Jul 7, 2016, at 10:56 PM, Ryan notifications@github.com wrote:

I actually have no idea. Formally, I am a "visiting scholar" at Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[rgiordan]

A couple students provided other examples of Berkeley students contributing
to high-profile open source projects (Theano and Apache Spark) as grad
students.

On Thu, Jul 7, 2016 at 5:09 PM, Bob Carpenter notifications@github.com
wrote:

Yes, it's blanket to any contribution to Stan now and in the future.

Berkeley's very liberal about allowing open-source. They're the
"B" in "BSD", after all. They're also the ones behind AmpLab.

Most universities seem to be OK with open source, though they
often ask you to verify. Columbia Tech Ventures in the end was surprised
we were asking them because they say they always allow researchers to
release
things open source if that's what they want to do. We could've saved
ourselves a lot of time had we gone to the top earlier.

And no university is going to think it needs to preserve rights to
patches to other software---there's nothing for them to gain from it.
It's the money trail, as usual.

• Bob

On Jul 7, 2016, at 5:00 PM, Michael Betancourt notifications@github.com
wrote:

I think it would be prudent — any relevant issues on the Columbia side
would be in any documents you signed. We had to go through significant
red tape to get the open source okay from Columbia and I don’t think it’s
blanket to any contribution to Stan, but perhaps someone can comment?
No idea if it’s any easier from the Berkeley side.

On Jul 7, 2016, at 10:56 PM, Ryan notifications@github.com wrote:

I actually have no idea. Formally, I am a "visiting scholar" at
Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If
not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <
notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited
testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[betanalpha]

Sure, I would think the B in BSD would be relevant and that
most universities would be okay with open source, but nothing
seems to be set in stone and if we’re trying to be careful moving
forward we might as well check where we can, no?

On Jul 7, 2016, at 11:09 PM, Bob Carpenter notifications@github.com wrote:

Yes, it's blanket to any contribution to Stan now and in the future.

Berkeley's very liberal about allowing open-source. They're the
"B" in "BSD", after all. They're also the ones behind AmpLab.

Most universities seem to be OK with open source, though they
often ask you to verify. Columbia Tech Ventures in the end was surprised
we were asking them because they say they always allow researchers to release
things open source if that's what they want to do. We could've saved
ourselves a lot of time had we gone to the top earlier.

And no university is going to think it needs to preserve rights to
patches to other software---there's nothing for them to gain from it.
It's the money trail, as usual.

• Bob

On Jul 7, 2016, at 5:00 PM, Michael Betancourt notifications@github.com wrote:

I think it would be prudent — any relevant issues on the Columbia side
would be in any documents you signed. We had to go through significant
red tape to get the open source okay from Columbia and I don’t think it’s
blanket to any contribution to Stan, but perhaps someone can comment?
No idea if it’s any easier from the Berkeley side.

On Jul 7, 2016, at 10:56 PM, Ryan notifications@github.com wrote:

I actually have no idea. Formally, I am a "visiting scholar" at Columbia
this summer, though I am paid by a Berkeley grant. Will that do? If not,
I can try to find out.

On Thu, Jul 7, 2016 at 4:52 PM, Michael Betancourt <notifications@github.com

wrote:

Just to be careful to confirm — does Berkeley grant
permission to release contributions under BSD3? Or
have your received an exception?

We just have to be careful as universities are starting
to get more strict about these things!

On Jul 7, 2016, at 9:37 PM, Ryan notifications@github.com wrote:

Submisison Checklist

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

Fixes #311

Intended Effect:

Inline functions allowing stan headers to be included in multiple
translation units.

How to Verify:

See example in #311

Side Effects:

Perhaps slightly longer compile times, though in my limited testing I
didn't notice a difference.

Documentation:

None.

Reviewer Suggestions:

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):
UC Berkeley

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/)
You can view, comment on, or merge this pull request online at:

#313

Commit Summary

fixes #307. Removing built documentation. [skip ci]
Inline instantiated functions.
Inline instantiated functions.
File Changes

M stan/math/prim/arr/fun/log_sum_exp.hpp (2)
M stan/math/prim/mat/fun/assign.hpp (2)
M stan/math/prim/mat/fun/csr_u_to_z.hpp (4)
M stan/math/prim/scal/fun/abs.hpp (2)
M stan/math/prim/scal/fun/digamma.hpp (2)
M stan/math/prim/scal/fun/gamma_p.hpp (2)
M stan/math/prim/scal/fun/gamma_q.hpp (2)
M stan/math/prim/scal/fun/grad_inc_beta.hpp (3)
M stan/math/prim/scal/fun/inc_beta_ddz.hpp (2)
M stan/math/prim/scal/fun/lgamma.hpp (2)
M stan/math/prim/scal/fun/log_mix.hpp (2)
M stan/math/rev/arr/functor/coupled_ode_system.hpp (2)
M stan/math/rev/core/precomputed_gradients.hpp (2)
M stan/math/rev/mat/fun/cholesky_decompose.hpp (24)
M stan/math/rev/mat/fun/grad.hpp (2)
M stan/math/rev/mat/fun/sd.hpp (2)
M stan/math/rev/mat/fun/stan_print.hpp (2)
M stan/math/rev/mat/fun/variance.hpp (4)
M stan/math/rev/scal/fun/grad_inc_beta.hpp (2)
M test/unit/math/fwd/mat/vectorize/expect_fwd_matrix_value.hpp (2)
Patch Links:

https://github.com/stan-dev/math/pull/313.patch
https://github.com/stan-dev/math/pull/313.diff
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[rgiordan]

@betanalpha , are you satisfied with the fact that Berkeley students have been contributing to open source projects for a while? Would you like me to cite specific examples? Or do you want to hear something from an official administrative body?

[betanalpha]

If Bob is fine then I’m fine, although anecdotal precedent seems tricky.

On Jul 9, 2016, at 9:42 PM, Ryan notifications@github.com wrote:

@betanalpha , are you satisfied with the fact that Berkeley students have been contributing to open source projects for a while? Would you like me to cite specific examples? Or do you want to hear something from an official administrative body?

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[syclik]

I'm ok with the IP issues here. I can't see anyone having a problem with ~20 additions of the inline keyword.

[syclik]

There were just a couple things I wanted to see:

• timing of compilation
• performance timing

Both can be informal and hopefully I'll get to it soon. We just want to make sure it doesn't add a lot of extra time to compilation or any time to performance.

[rgiordan]

That makes sense. LMK if I can help. I only have one stan model sitting around (it's the one here), and it didn't make a noticeable difference. Hopefully you have some ideas about what would be a more meaningful test suite.

[syclik]

Thanks. This is all ad hoc testing for the moment. We really need to put together a better testing suite.

(I'm always hoping I run into some literature and implementations on how to do this reliably, but haven't found it.)

[syclik]

Jenkins, retest this please.

[syclik]

I verified that this patch doesn't increase the build time or compilation time, at least to anything we can measure reliably.

I ran each of these things 100 times:

1. Compile a model with one of the inlined functions (example-models/basic_estimators/normal_mixture.stan)
2. Compile a model without one of the inlined functions (example-models/bugs_examples/vol1/blocker/blocker.stan)
3. Run a model with one of the inlined functions for 10 different seeds
4. Run a model without one of the inlined functions for 10 different seeds.

I'm looking at the results and half the tasks are faster and half are slower, but all within a couple percent or less, so I don't think I'm seeing anything systematic.

[syclik]

I'll merge this once the tests pass.

[rgiordan]

Thanks, Daniel!

On Tue, Jul 19, 2016 at 3:49 PM, Daniel Lee notifications@github.com
wrote:

I'll merge this once the tests pass.

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