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Clang tidy cleanup and using std algorithms #1373

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Clang tidy cleanup and using std algorithms #1373

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b9f545b
Clang tidy with modernize-use-equals-default,readability-braces-aroun…
SteveBronder Sep 30, 2019
4064902
Adds range based for loops via clang tidy, accumulates in log_sum_exp…
SteveBronder Sep 30, 2019
23706ed
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot Sep 30, 2019
bade075
include <numeric> in dot_self header
SteveBronder Sep 30, 2019
8a2dff8
Merge branch 'clang-tidy/braces-defaults_constructor-range_for_loops'…
SteveBronder Sep 30, 2019
2407b7a
copy-pasted an accumulate without changing the variable names from on…
SteveBronder Sep 30, 2019
8bb5458
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot Sep 30, 2019
0c31b37
fix headers
SteveBronder Sep 30, 2019
d68129f
forgot accumulate is in numeric and not algorithm
SteveBronder Sep 30, 2019
f9275d1
test in scal was using unitialized vector?
SteveBronder Sep 30, 2019
06c465a
merge to develop
SteveBronder Oct 8, 2019
bdadd8e
cleanups for promote_elements
SteveBronder Oct 8, 2019
8656836
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot Oct 8, 2019
d716461
remove tbb stuff that should be ignored
SteveBronder Oct 8, 2019
3266349
Use auto in gp_exp_quad_cov, add rule of 5 to accumulator, and pass b…
SteveBronder Nov 3, 2019
90be53e
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot Nov 3, 2019
c9fef6c
merge to develop
SteveBronder Nov 5, 2019
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[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/… 
…stable/2017-11-14)
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@stan-buildbot
stan-buildbot committed Nov 3, 2019
commit 90be53e03fd2352be125d54ec8838282942f77ca
83 changes: 38 additions & 45 deletions stan/math/prim/mat/fun/gp_exp_quad_cov.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,8 @@ namespace internal {
* @return squared distance
*/
template <typename T_x, typename T_sigma, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma_sq,
const T_l &neg_half_inv_l_sq) {
inline auto gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma_sq,
const T_l &neg_half_inv_l_sq) {
using std::exp;
const size_t x_size = x.size();
Eigen::Matrix<return_type_t<T_x, T_sigma, T_l>, Eigen::Dynamic,
Expand Down Expand Up @@ -69,9 +68,8 @@ gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma_sq,
* x is nan or infinite
*/
template <typename T_x, typename T_sigma>
inline auto
gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
const T_sigma &sigma_sq) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
const T_sigma &sigma_sq) {
using std::exp;
const auto x_size = x.size();
Eigen::Matrix<return_type_t<T_x, T_sigma>, Eigen::Dynamic, Eigen::Dynamic>
Expand Down Expand Up @@ -105,9 +103,10 @@ gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
* @return squared distance
*/
template <typename T_x1, typename T_x2, typename T_sigma, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<T_x1> &x1, const std::vector<T_x2> &x2,
const T_sigma &sigma_sq, const T_l &neg_half_inv_l_sq) {
inline auto gp_exp_quad_cov(const std::vector<T_x1> &x1,
const std::vector<T_x2> &x2,
const T_sigma &sigma_sq,
const T_l &neg_half_inv_l_sq) {
using std::exp;
Eigen::Matrix<return_type_t<T_x1, T_x2, T_sigma, T_l>, Eigen::Dynamic,
Eigen::Dynamic>
Expand Down Expand Up @@ -137,10 +136,9 @@ gp_exp_quad_cov(const std::vector<T_x1> &x1, const std::vector<T_x2> &x2,
* @return squared distance
*/
template <typename T_x1, typename T_x2, typename T_s>
inline auto
gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
const std::vector<Eigen::Matrix<T_x2, -1, 1>> &x2,
const T_s &sigma_sq) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
const std::vector<Eigen::Matrix<T_x2, -1, 1>> &x2,
const T_s &sigma_sq) {
using std::exp;
Eigen::Matrix<return_type_t<T_x1, T_x2, T_s>, Eigen::Dynamic, Eigen::Dynamic>
cov(x1.size(), x2.size());
Expand Down Expand Up @@ -169,9 +167,8 @@ gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
* x is nan or infinite
*/
template <typename T_x, typename T_sigma, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma,
const T_l &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma,
const T_l &length_scale) {
check_positive("gp_exp_quad_cov", "magnitude", sigma);
check_positive("gp_exp_quad_cov", "length scale", length_scale);

Expand Down Expand Up @@ -208,9 +205,9 @@ gp_exp_quad_cov(const std::vector<T_x> &x, const T_sigma &sigma,
* x is nan or infinite
*/
template <typename T_x, typename T_sigma, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
const T_sigma &sigma, const std::vector<T_l> &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
const T_sigma &sigma,
const std::vector<T_l> &length_scale) {
check_positive_finite("gp_exp_quad_cov", "magnitude", sigma);
check_positive_finite("gp_exp_quad_cov", "length scale", length_scale);

Expand Down Expand Up @@ -250,9 +247,9 @@ gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x, -1, 1>> &x,
* x is nan or infinite
*/
template <typename T_x1, typename T_x2, typename T_sigma, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<T_x1> &x1, const std::vector<T_x2> &x2,
const T_sigma &sigma, const T_l &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<T_x1> &x1,
const std::vector<T_x2> &x2, const T_sigma &sigma,
const T_l &length_scale) {
const char *function_name = "gp_exp_quad_cov";
check_positive(function_name, "magnitude", sigma);
check_positive(function_name, "length scale", length_scale);
Expand Down Expand Up @@ -298,10 +295,10 @@ gp_exp_quad_cov(const std::vector<T_x1> &x1, const std::vector<T_x2> &x2,
* x is nan or infinite
*/
template <typename T_x1, typename T_x2, typename T_s, typename T_l>
inline auto
gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
const std::vector<Eigen::Matrix<T_x2, -1, 1>> &x2,
const T_s &sigma, const std::vector<T_l> &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
const std::vector<Eigen::Matrix<T_x2, -1, 1>> &x2,
const T_s &sigma,
const std::vector<T_l> &length_scale) {
size_t x1_size = x1.size();
size_t x2_size = x2.size();
size_t l_size = length_scale.size();
Expand Down Expand Up @@ -345,9 +342,8 @@ gp_exp_quad_cov(const std::vector<Eigen::Matrix<T_x1, -1, 1>> &x1,
* x is nan or infinite
*/
template <>
inline auto gp_exp_quad_cov(const std::vector<double> &x,
const double &sigma,
const double &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<double> &x, const double &sigma,
const double &length_scale) {
const char *function_name = "gp_exp_quad_cov";
check_positive(function_name, "magnitude", sigma);
check_positive(function_name, "length scale", length_scale);
Expand Down Expand Up @@ -389,8 +385,7 @@ inline auto gp_exp_quad_cov(const std::vector<double> &x,
*/
template <>
inline auto gp_exp_quad_cov(const std::vector<Eigen::VectorXd> &x,
const double &sigma,
const double &length_scale) {
const double &sigma, const double &length_scale) {
const char *function_name = "gp_exp_quad_cov";
check_positive(function_name, "magnitude", sigma);
check_positive(function_name, "length scale", length_scale);
Expand Down Expand Up @@ -432,9 +427,9 @@ inline auto gp_exp_quad_cov(const std::vector<Eigen::VectorXd> &x,
* x is nan or infinite
*/
template <>
inline auto gp_exp_quad_cov(
const std::vector<Eigen::VectorXd> &x, const double &sigma,
const std::vector<double> &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::VectorXd> &x,
const double &sigma,
const std::vector<double> &length_scale) {
const char *function_name = "gp_exp_quad_cov";
check_positive_finite(function_name, "magnitude", sigma);
check_positive_finite(function_name, "length scale", length_scale);
Expand Down Expand Up @@ -480,9 +475,8 @@ inline auto gp_exp_quad_cov(
*/
template <>
inline auto gp_exp_quad_cov(const std::vector<double> &x1,
const std::vector<double> &x2,
const double &sigma,
const double &length_scale) {
const std::vector<double> &x2, const double &sigma,
const double &length_scale) {
const char *function_name = "gp_exp_quad_cov";
check_positive_finite(function_name, "magnitude", sigma);
check_positive_finite(function_name, "length scale", length_scale);
Expand Down Expand Up @@ -530,10 +524,9 @@ inline auto gp_exp_quad_cov(const std::vector<double> &x1,
* x is nan or infinite
*/
template <>
inline auto gp_exp_quad_cov(
const std::vector<Eigen::VectorXd> &x1,
const std::vector<Eigen::VectorXd> &x2, const double &sigma,
const double &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::VectorXd> &x1,
const std::vector<Eigen::VectorXd> &x2,
const double &sigma, const double &length_scale) {
const char *function_name = "gp_exp_quad_cov";
const int x1_size = x1.size();
const int x2_size = x2.size();
Expand Down Expand Up @@ -586,10 +579,10 @@ inline auto gp_exp_quad_cov(
* x is nan or infinite
*/
template <>
inline auto gp_exp_quad_cov(
const std::vector<Eigen::VectorXd> &x1,
const std::vector<Eigen::VectorXd> &x2, const double &sigma,
const std::vector<double> &length_scale) {
inline auto gp_exp_quad_cov(const std::vector<Eigen::VectorXd> &x1,
const std::vector<Eigen::VectorXd> &x2,
const double &sigma,
const std::vector<double> &length_scale) {
size_t x1_size = x1.size();
size_t x2_size = x2.size();
size_t l_size = length_scale.size();
Expand Down