Merge commit '2e87ecadc075bab42fd7a51178ce33ae2f6c3ccc' into HEAD

Author: yashikno

.git-blame-ignore-revs

@@ -25,4 +25,4 @@ If this is a **feature request**, show what you expect to happen if the feature
 
 
 #### Current Version:
-v4.6.1
+v4.6.2

.github/ISSUE_TEMPLATE.md

@@ -1,5 +1,11 @@
 Stan Math Library Release Notes
 
+======================================================================
+v4.6.2 (15 May 2023)
+======================================================================
+
+- Fix an issue in Stan, see release notes.
+
 ======================================================================
 v4.6.1 (2 May 2023)
 ======================================================================

RELEASE-NOTES.txt

@@ -1,4 +1,4 @@
-# Developers Guide {#developer_guide}
+# Developer Guide {#developer_guide}
 
 Thanks for checking out these docs. This is where you'll find information on contributing to the [Math library](https://github.com/stan-dev/math), how the source code is laid out, and other technical details that could help. This wiki focuses on things relevant to the Math library. There's also a separate [Stan wiki](https://github.com/stan-dev/stan/wiki) for things related to the language, services, algorithms.
 
@@ -41,7 +41,7 @@ For implementation details of the Math library's automatic differentiation, plea
 
 We're committed to having a permissive open-source license. The Math library is [licensed with the BSD 3-Clause License](https://github.com/stan-dev/math/blob/develop/LICENSE%2Emd) and we only accept changes to the code base that compatible with this license.
 
-# Contributing {#contribution}
+# Contributing {#contributing}
 
 Thanks for reading! We love contributions from everyone in the form of good discussion, issues, and pull requests.
 

doxygen/contributor_help_pages/developer_doc.md

@@ -1,24 +1,46 @@
 <doxygenlayout version="1.0">
 <navindex>
   <tab type="user" url="index.html" title="Overview" />
+  <!-- Note: @ref doesn't work in doxygen v1.9.7. Perhaps this could come back in the future.
   <tab type="usergroup" visible="yes" title="Contributor Guides" url="@ref contributing" intro="">
-      <tab type="usergroup" visible="yes" title="Developer Guide" url="@ref developer_guide" intro=""/>
-      <tab type="usergroup" visible="yes" title="Adding New Functions" url="@ref getting_started" intro=""/>
-      <tab type="usergroup" visible="yes" title="Adding New Distributions" url="@ref new_distribution" intro=""/>
-      <tab type="usergroup" visible="yes" title="Common Pitfalls" url="@ref common_pitfalls" intro=""/>
-      <tab type="usergroup" visible="yes" title="Using requires for general overloads" url="@ref require_meta_doc" intro=""/>
-      <tab type="usergroup" visible="yes" title="Reverse Mode Types" url="@ref reverse_mode_types" intro=""/>
-      <tab type="usergroup" visible="yes" title="Testing Automatic Differentiation Functions" url="@ref autodiff_test_guide" intro=""/>
-      <tab type="usergroup" visible="yes" title="Testing New Distributions" url="@ref dist_tests" intro=""/>
-      <tab type="usergroup" visible="yes" title="Add New Functions With Known Gradients" url="@ref new_grad" intro=""/>
-      <tab type="usergroup" visible="yes" title="Adding New OpenCL Functions" url="@ref opencl_guide" intro=""/>
-      <tab type="usergroup" visible="yes" title="Windows Development Tips" url="@ref windows_tips" intro=""/>
-  </tab>
+      <tab type="user" visible="yes" title="Developer Guide" url="@ref developer_guide" intro=""/>
+      <tab type="user" visible="yes" title="Adding New Functions" url="@ref getting_started" intro=""/>
+      <tab type="user" visible="yes" title="Adding New Distributions" url="@ref new_distribution" intro=""/>
+      <tab type="user" visible="yes" title="Common Pitfalls" url="@ref common_pitfalls" intro=""/>
+      <tab type="user" visible="yes" title="Using requires for general overloads" url="@ref require_meta_doc" intro=""/>
+      <tab type="user" visible="yes" title="Reverse Mode Types" url="@ref reverse_mode_types" intro=""/>
+      <tab type="user" visible="yes" title="Testing Automatic Differentiation Functions" url="@ref autodiff_test_guide" intro=""/>
+      <tab type="user" visible="yes" title="Testing New Distributions" url="@ref dist_tests" intro=""/>
+      <tab type="user" visible="yes" title="Add New Functions With Known Gradients" url="@ref new_grad" intro=""/>
+      <tab type="user" visible="yes" title="Adding New OpenCL Functions" url="@ref opencl_guide" intro=""/>
+      <tab type="user" visible="yes" title="Windows Development Tips" url="@ref windows_tips" intro=""/>
+  </tab> 
+  -->
+  <tab type="usergroup" visible="yes" title="Contributor Guides" url="md__8github_2_c_o_n_t_r_i_b_u_t_i_n_g.html" intro="">
+      <tab type="user" visible="yes" title="Developer Guide" url="md_doxygen_2contributor__help__pages_2developer__doc.html" intro=""/>
+      <tab type="user" visible="yes" title="Adding New Functions" url="md_doxygen_2contributor__help__pages_2getting__started.html" intro=""/>
+      <tab type="user" visible="yes" title="Adding New Distributions" url="md_doxygen_2contributor__help__pages_2adding__new__distributions.html" intro=""/>
+      <tab type="user" visible="yes" title="Common Pitfalls" url="md_doxygen_2contributor__help__pages_2common__pitfalls.html" intro=""/>
+      <tab type="user" visible="yes" title="Using requires for general overloads" url="md_doxygen_2contributor__help__pages_2require__meta.html" intro=""/>
+      <tab type="user" visible="yes" title="Reverse Mode Types" url="md_doxygen_2contributor__help__pages_2reverse__mode__types.html" intro=""/>
+      <tab type="user" visible="yes" title="Testing Automatic Differentiation Functions" url="md_doxygen_2contributor__help__pages_2autodiff__test__guide.html" intro=""/>
+      <tab type="user" visible="yes" title="Testing New Distributions" url="md_doxygen_2contributor__help__pages_2distribution__tests.html" intro=""/>
+      <tab type="user" visible="yes" title="Add New Functions With Known Gradients" url="md_doxygen_2contributor__help__pages_2new__gradients.html" intro=""/>
+      <tab type="user" visible="yes" title="Adding New OpenCL Functions" url="md_doxygen_2contributor__help__pages_2add__new__opencl__kernel.html" intro=""/>
+      <tab type="user" visible="yes" title="Windows Development Tips" url="md_doxygen_2contributor__help__pages_2windows__devnotes.html" intro=""/>
+  </tab> 
   <tab type="modules" visible="yes" title="Internal Docs" intro=""/>
+  <!-- Note: @ref doesn't work in doxygen v1.9.7. Perhaps this could come back in the future.
+  <tab type="usergroup" visible="yes" title="Parallelism" intro="">
+    <tab type="user" visible="yes" title="Threading" url="@ref tbb_threading" intro=""/>
+    <tab type="user" visible="yes" title="OpenCL for GPU Computing" url="@ref opencl_support" intro=""/>
+    <tab type="user" visible="yes" title="MPI Support" url="@ref mpi" intro=""/>
+  </tab>
+  -->
   <tab type="usergroup" visible="yes" title="Parallelism" intro="">
-    <tab type="usergroup" visible="yes" title="Threading" url="@ref tbb_threading" intro=""/>
-    <tab type="usergroup" visible="yes" title="OpenCL for GPU Computing" url="@ref opencl_support" intro=""/>
-    <tab type="usergroup" visible="yes" title="MPI Support" url="@ref mpi" intro=""/>
+    <tab type="user" visible="yes" title="Threading" url="md_doxygen_2parallelism__support_2threading__tbb.html" intro=""/>
+    <tab type="user" visible="yes" title="OpenCL for GPU Computing" url="md_doxygen_2parallelism__support_2opencl__support.html" intro=""/>
+    <tab type="user" visible="yes" title="MPI Support" url="md_doxygen_2parallelism__support_2mpi__parallelism.html" intro=""/>
   </tab>
   <tab type="usergroup" visible="yes" title="(External Link) Stan Language Docs" url="https://mc-stan.org/users/documentation/" intro=""/>
   <tab type="usergroup" visible="yes" title="(External Link) Stan Discourse" url="https://discourse.mc-stan.org/" intro=""/>

doxygen/doxygen.cfg

@@ -112,7 +112,7 @@ git commit -m "upgrading to boost v${boost_version}; adding unmodified boost lib
 cd boost_${boost_version}
 
 git rm -rf boost.css boost.png index.htm index.html INSTALL rst.css --ignore-unmatch
-git rm -rf doc/ libs/*/test/ libs/*/example/ libs/*/doc/ --ignore-unmatch
+git rm -rf doc/ libs/*/test/ libs/*/example/ libs/*/doc/ libs/*/*/doc/ --ignore-unmatch
 git rm -rf boost/leaf/ libs/leaf/ boost/nowide/ libs/nowide --ignore-unmatch 
 git rm -rf boost/pfr libs/pfr boost/json/ libs/json/ --ignore-unmatch
 git rm -rf boost/static_string libs/static_string --ignore-unmatch

doxygen/pretty_stuff/layout.xml

@@ -58,7 +58,7 @@ ifneq (,$(findstring g++,$(CXX)))
   CXX_TYPE ?= gcc
 endif
 CXX_TYPE ?= other
-CXX_VERSION :=  $(shell $(CXX) -dumpversion 2>&1)
+CXX_VERSION :=  $(shell $(CXX) -dumpfullversion -dumpversion 2>&1)
 CXX_MAJOR := $(word 1,$(subst ., ,$(CXX_VERSION)))
 CXX_MINOR := $(word 2,$(subst ., ,$(CXX_VERSION)))