Generalize view and size functions #1660

t4c1 · 2020-01-30T12:08:33Z

Summary

Generalizes inputs to view and size functions (col, row, sub_col, sub_row, head, tail, diagonal, transpose, cols, rows, num_elements, dims).

Tests

This is a refactor so no new tests.

Side Effects

None.

Checklist

Math issue Generalize matrix function signatures #1470
Copyright holder: Tadej Ciglarič

The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the 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/)
the basic tests are passing
- unit tests pass (to run, use: ./runTests.py test/unit)
- header checks pass, (make test-headers)
- dependencies checks pass, (make test-math-dependencies)
- docs build, (make doxygen)
- code passes the built in C++ standards checks (make cpplint)
the code is written in idiomatic C++ and changes are documented in the doxygen
the new changes are tested

…gs/RELEASE_500/final)

t4c1 · 2020-01-30T12:45:56Z

I think this error will be gone once #1628 is merged in.

# Conflicts: # stan/math/prim/fun/cols.hpp # stan/math/prim/fun/transpose.hpp

stan-buildbot · 2020-02-17T19:27:17Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	5.06	5.12	0.99	-1.14% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.99	-0.62% slower
eight_schools/eight_schools.stan	0.09	0.1	0.9	-10.98% slower
gp_regr/gp_regr.stan	0.22	0.22	1.0	-0.08% slower
irt_2pl/irt_2pl.stan	6.05	6.1	0.99	-0.79% slower
performance.compilation	89.45	87.2	1.03	2.52% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.49	7.47	1.0	0.2% faster
pkpd/one_comp_mm_elim_abs.stan	21.24	20.78	1.02	2.21% faster
sir/sir.stan	89.84	96.38	0.93	-7.28% slower
gp_regr/gen_gp_data.stan	0.05	0.05	0.99	-1.16% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.01	2.99	1.01	0.61% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.32	0.99	-1.46% slower
arK/arK.stan	1.74	1.74	1.0	-0.31% slower
arma/arma.stan	0.79	0.79	1.0	-0.04% slower
garch/garch.stan	0.58	0.59	0.99	-0.67% slower
Mean result: 0.98850650244

Jenkins Console Log
Blue Ocean
Commit hash: 59335f6

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

t4c1 · 2020-02-18T13:24:36Z

This is now ready for a review.

rok-cesnovar

This is missing some tests then its good to go. I flagged all functions that need them.

rok-cesnovar · 2020-02-19T10:29:32Z

stan/math/prim/err/check_vector_index.hpp

+ * @throw <code>std::out_of_range</code> if the index is out of range.
+ */
+template <typename T, typename = require_eigen_vector_t<T>>
+inline void check_vector_index(const char* function, const char* name,


This function is missing tests.

stan/math/prim/fun/col.hpp

stan/math/prim/fun/diagonal.hpp

stan/math/prim/fun/head.hpp

stan/math/prim/fun/row.hpp

stan/math/prim/fun/sub_col.hpp

stan/math/prim/fun/sub_row.hpp

stan/math/prim/fun/tail.hpp

stan-buildbot · 2020-02-20T15:59:22Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.79	5.0	0.96	-4.43% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.02	1.82% faster
eight_schools/eight_schools.stan	0.09	0.09	0.94	-6.88% slower
gp_regr/gp_regr.stan	0.22	0.23	0.96	-4.67% slower
irt_2pl/irt_2pl.stan	6.08	6.24	0.97	-2.57% slower
performance.compilation	88.18	88.44	1.0	-0.29% slower
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.3	7.49	0.98	-2.5% slower
pkpd/one_comp_mm_elim_abs.stan	20.8	21.95	0.95	-5.54% slower
sir/sir.stan	90.12	91.88	0.98	-1.95% slower
gp_regr/gen_gp_data.stan	0.04	0.05	0.98	-1.88% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.99	3.06	0.98	-2.52% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.33	0.31	1.04	3.66% faster
arK/arK.stan	1.74	1.79	0.98	-2.44% slower
arma/arma.stan	0.76	0.81	0.94	-6.63% slower
garch/garch.stan	0.53	0.54	0.97	-3.49% slower
Mean result: 0.974562119405

Jenkins Console Log
Blue Ocean
Commit hash: c98fa84

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

rok-cesnovar

Thanks for adding tests.

t4c1 and others added 4 commits January 30, 2020 12:57

generalized view and size functions

d31d678

added missing file

ddef4aa

fixes to doxygen

57baa35

[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…

458b8dc

…gs/RELEASE_500/final)

Merge branch 'develop' into generalize_view_and_size

59335f6

# Conflicts: # stan/math/prim/fun/cols.hpp # stan/math/prim/fun/transpose.hpp

rok-cesnovar requested changes Feb 19, 2020

View reviewed changes

added test for check_vector_index

c98fa84

rok-cesnovar approved these changes Feb 24, 2020

View reviewed changes

rok-cesnovar merged commit cdb9d14 into stan-dev:develop Feb 24, 2020

rok-cesnovar deleted the generalize_view_and_size branch February 24, 2020 07:44

SteveBronder mentioned this pull request Apr 16, 2020

Stan Math 3.2 release #1826

Closed

bbbales2 mentioned this pull request Apr 20, 2020

Stanc3 release for Cmdstan 2.23 stan-dev/stanc3#498

Closed

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Generalize view and size functions #1660

Generalize view and size functions #1660

t4c1 commented Jan 30, 2020 •

edited

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t4c1 commented Jan 30, 2020

stan-buildbot commented Feb 17, 2020

t4c1 commented Feb 18, 2020

rok-cesnovar left a comment

rok-cesnovar Feb 19, 2020

stan-buildbot commented Feb 20, 2020

rok-cesnovar left a comment

Generalize view and size functions #1660

Generalize view and size functions #1660

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t4c1 commented Jan 30, 2020 • edited Loading

Summary

Tests

Side Effects

Checklist

t4c1 commented Jan 30, 2020

stan-buildbot commented Feb 17, 2020

t4c1 commented Feb 18, 2020

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rok-cesnovar Feb 19, 2020

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t4c1 commented Jan 30, 2020 •

edited

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