Cleanup/1886 cleanup global space in prim tests, replace pull_msg with expect_throw_msg #1947

rok-cesnovar · 2020-06-22T19:58:30Z

Summary

This PR advances #1886 with the following:

cleaned up /prim tests files of global using statements
remove the unnecesarry pull_msg functions in the gp_* tests. They can be replaced with EXPECT_THROW_MSG.
puts functions with non-unique names file f, fun, f1 in namespaces (The namespace names are based on the file name)
removed global variables like const char* function_ = "function"; from the global namespace of tests
moved util functions like correct_type_vector in the utils header file
added missing header guards to test utility files (ode mock observers and hmm test utilities)

No release notes as this is part of an ongoing project that is being done over multiple PRs. Will put release notes in the final one.

Tests

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Side Effects

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Checklist

Math issue Organize and cleanup the use of utils in test/ #1886
Copyright holder: Rok Češnovar, Univ. of Ljubljana

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

…util-cleanup-part2

…4.1 (tags/RELEASE_600/final)

…util-cleanup-part2

…s/RELEASE_600/final)

…-part2" This reverts commit 609c7a6, reversing changes made to 2e3f863. # Conflicts: # runTests.py

This reverts commit 3f7c339.

stan-buildbot · 2020-06-23T16:50:31Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.94	4.05	1.22	17.99% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.03	2.94% faster
eight_schools/eight_schools.stan	0.21	0.09	2.31	56.65% faster
gp_regr/gp_regr.stan	0.2	0.2	1.03	3.14% faster
irt_2pl/irt_2pl.stan	5.57	5.5	1.01	1.24% faster
performance.compilation	89.61	87.0	1.03	2.91% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.86	7.93	0.99	-0.83% slower
pkpd/one_comp_mm_elim_abs.stan	27.12	20.99	1.29	22.6% faster
sir/sir.stan	113.21	91.12	1.24	19.51% faster
gp_regr/gen_gp_data.stan	0.05	0.05	1.03	2.5% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.18	3.09	1.03	2.77% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.61	0.33	1.85	46.0% faster
arK/arK.stan	2.86	2.48	1.15	13.13% faster
arma/arma.stan	0.67	0.62	1.08	7.56% faster
garch/garch.stan	1.1	0.6	1.84	45.55% faster
Mean result: 1.27556116968

Jenkins Console Log
Blue Ocean
Commit hash: 6fe1529

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 · 2020-07-02T10:48:42Z

test/unit/math/prim/fun/gp_exponential_cov_test.cpp

+  EXPECT_THROW_MSG(stan::math::gp_exponential_cov(x_2, x_2, sigma_bad, l_bad),
+                   std::domain_error, " magnitude");


[optional] I think we should remove all these tests that expect specific error message when multiple arguments have errors.

Good call, yeah. Will change just to expect throw.

t4c1 · 2020-07-02T11:23:47Z

test/unit/util.hpp

+namespace stan {
+namespace test {
+template <int R, int C>
+void correct_type_vector(const Eigen::Matrix<double, R, C>& x) {


[optional] I think a better name would be expect_type_vector.

…s/RELEASE_600/final)

t4c1

There are a few more of these tests that expect specific messages from multiple errors

test/unit/math/prim/fun/gp_exponential_cov_test.cpp

test/unit/math/prim/fun/gp_periodic_cov_test.cpp

test/unit/math/prim/fun/cov_exp_quad_test.cpp

rok-cesnovar · 2020-07-02T12:31:39Z

Thanks. Done.

…s/RELEASE_600/final)

stan-buildbot · 2020-07-02T19:00:49Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.13	4.04	1.02	2.3% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.0	-0.4% slower
eight_schools/eight_schools.stan	0.09	0.09	1.02	2.01% faster
gp_regr/gp_regr.stan	0.19	0.19	0.99	-0.99% slower
irt_2pl/irt_2pl.stan	5.23	5.37	0.97	-2.58% slower
performance.compilation	85.68	84.9	1.01	0.91% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.7	7.68	1.0	0.25% faster
pkpd/one_comp_mm_elim_abs.stan	20.36	20.96	0.97	-2.95% slower
sir/sir.stan	103.29	101.8	1.01	1.44% faster
gp_regr/gen_gp_data.stan	0.04	0.05	0.98	-1.61% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.19	3.02	1.06	5.34% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.32	0.99	-0.66% slower
arK/arK.stan	2.42	2.42	1.0	0.0% slower
arma/arma.stan	0.6	0.6	1.0	-0.07% slower
garch/garch.stan	0.52	0.52	1.0	0.28% faster
Mean result: 1.00259275639

Jenkins Console Log
Blue Ocean
Commit hash: 63b873e

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 and others added 30 commits May 26, 2020 16:27

cleanup pull_msg from gp_ tests

7f3a1ea

Merge remote-tracking branch 'origin/develop' into cleanup/1886-test-…

68eea50

…util-cleanup-part2

cleaned up prim/functor

ea9a8f5

cleaned up prim/meta

85945d6

cleaned up prim/err

8e11862

cleaned up prim/prob

c5335a9

cleaned up prim/fun

73a09a8

log mix test

9554327

Merge commit 'de6e454a7db5854c413dbb943a5a4f056d9085ec' into HEAD

8e54edc

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…

d2bf577

…4.1 (tags/RELEASE_600/final)

Merge remote-tracking branch 'origin/develop' into cleanup/1886-test-…

cc0a815

…util-cleanup-part2

fix namespace errors

5c7cc03

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…

3dff203

…s/RELEASE_600/final)

mising namespace

b00d550

namespace fix

2e4066c

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…

62ab0c6

…s/RELEASE_600/final)

jumbo init

ad9a559

fix namespace use in log_mix

eb2623f

more fix tests

2e3f863

Merge branch 'jumbotests' into cleanup/1886-test-util-cleanup-part2

609c7a6

add jumbo

3f7c339

missing namespace in categorical test

3035dcd

fix eigen namespace

3ed6342

fix missing Eigen

f3af9d0

add header guards

6aae15b

cleanup global namespace

87770b4

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…

8f584bc

…s/RELEASE_600/final)

Revert "Merge branch 'jumbotests' into cleanup/1886-test-util-cleanup…

7866ca9

…-part2" This reverts commit 609c7a6, reversing changes made to 2e3f863. # Conflicts: # runTests.py

Revert "add jumbo"

d3f7fb6

This reverts commit 3f7c339.

include prim/fun/eigen in utils

6fe1529

rok-cesnovar marked this pull request as ready for review June 23, 2020 12:50

rok-cesnovar mentioned this pull request Jun 23, 2020

Use jumbo tests #1948

Closed

t4c1 previously approved these changes Jul 2, 2020

View reviewed changes

rok-cesnovar added 2 commits July 2, 2020 13:52

dont test exact message for multiple bad args

34c24f1

replace correct_type_* with expect_type_*

8c57e24

rok-cesnovar dismissed t4c1’s stale review via 8c57e24 July 2, 2020 11:53

rok-cesnovar requested a review from t4c1 July 2, 2020 11:55

yashikno and others added 2 commits July 2, 2020 08:09

Merge commit '844c61f6a2b7c5faf21f72084849557206998d99' into HEAD

5ec9ef3

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…

bdbd7f7

…s/RELEASE_600/final)

t4c1 reviewed Jul 2, 2020

View reviewed changes

more exact message tests for multiple bad args removed

29592cf

[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…

63b873e

…s/RELEASE_600/final)

t4c1 approved these changes Jul 2, 2020

View reviewed changes

rok-cesnovar merged commit 7a800b6 into develop Jul 2, 2020

rok-cesnovar deleted the cleanup/1886-test-util-cleanup-part2 branch July 2, 2020 19:09

andrjohns mentioned this pull request Aug 9, 2020

Feature/elementwise checks revert revert #2007

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Cleanup/1886 cleanup global space in prim tests, replace pull_msg with expect_throw_msg #1947

Cleanup/1886 cleanup global space in prim tests, replace pull_msg with expect_throw_msg #1947

rok-cesnovar commented Jun 22, 2020 •

edited

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stan-buildbot commented Jun 23, 2020

t4c1 Jul 2, 2020

rok-cesnovar Jul 2, 2020

t4c1 Jul 2, 2020

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rok-cesnovar commented Jul 2, 2020

stan-buildbot commented Jul 2, 2020

		EXPECT_THROW_MSG(stan::math::gp_exponential_cov(x_2, x_2, sigma_bad, l_bad),
		std::domain_error, " magnitude");

Cleanup/1886 cleanup global space in prim tests, replace pull_msg with expect_throw_msg #1947

Cleanup/1886 cleanup global space in prim tests, replace pull_msg with expect_throw_msg #1947

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rok-cesnovar commented Jun 22, 2020 • edited Loading

Summary

Tests

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Checklist

stan-buildbot commented Jun 23, 2020

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rok-cesnovar commented Jun 22, 2020 •

edited

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