Merge branch 'develop' into generalize_fun_s_t

# Conflicts:
#	stan/math/prim/fun/mdivide_left_ldlt.hpp

Author: t4c1

.github/ISSUE_TEMPLATE.md

@@ -25,4 +25,4 @@ If this is a **feature request**, show what you expect to happen if the feature
 
 
 #### Current Version:
-v3.1.0
+v3.2.0

RELEASE-NOTES.txt

@@ -51,7 +51,7 @@ BIT=32
 ```
 If the test suite isn't built first, client code using numerical integration routines such as `integrate_ode_bdf` may fail to link because the libraries haven't been built yet. Obviously these files and directories would need to be added to the downstream project makefile's LDLIBS variable, or equivalent.
 ```
-$ make lib/sundials_3.1.0/lib/libsundials_cvodes.a lib/sundials_3.1.0/lib/libsundials_nvecserial.a
-make: 'lib/sundials_3.1.0/lib/libsundials_cvodes.a' is up to date.
-make: 'lib/sundials_3.1.0/lib/libsundials_nvecserial.a' is up to date.
+$ make lib/sundials_3.2.0/lib/libsundials_cvodes.a lib/sundials_3.2.0/lib/libsundials_nvecserial.a
+make: 'lib/sundials_3.2.0/lib/libsundials_cvodes.a' is up to date.
+make: 'lib/sundials_3.2.0/lib/libsundials_nvecserial.a' is up to date.
 ```

doxygen/contributor_help_pages/windows_devnotes.md

@@ -38,7 +38,7 @@ PROJECT_NAME           = "Stan Math Library"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 3.1.0
+PROJECT_NUMBER         = 3.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -133,7 +133,7 @@ ALWAYS_DETAILED_SEC    = NO
 # operators of the base classes will not be shown.
 # The default value is: NO.
 
-INLINE_INHERITED_MEMB  = NO
+INLINE_INHERITED_MEMB  = YES
 
 # If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
 # before files name in the file list and in the header files. If set to NO the
@@ -341,14 +341,14 @@ IDL_PROPERTY_SUPPORT   = YES
 # all members of a group must be documented explicitly.
 # The default value is: NO.
 
-DISTRIBUTE_GROUP_DOC   = NO
+DISTRIBUTE_GROUP_DOC   = YES
 
 # If one adds a struct or class to a group and this option is enabled, then also
 # any nested class or struct is added to the same group. By default this option
 # is disabled and one has to add nested compounds explicitly via \ingroup.
 # The default value is: NO.
 
-GROUP_NESTED_COMPOUNDS = NO
+GROUP_NESTED_COMPOUNDS = YES
 
 # Set the SUBGROUPING tag to YES to allow class member groups of the same type
 # (for instance a group of public functions) to be put as a subgroup of that
@@ -378,7 +378,7 @@ INLINE_GROUPED_CLASSES = NO
 # Man pages) or section (for LaTeX and RTF).
 # The default value is: NO.
 
-INLINE_SIMPLE_STRUCTS  = NO
+INLINE_SIMPLE_STRUCTS  = YES
 
 # When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
 # enum is documented as struct, union, or enum with the name of the typedef. So
@@ -422,7 +422,7 @@ EXTRACT_ALL            = YES
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -743,7 +743,7 @@ WARN_NO_PARAMDOC       = NO
 # a warning is encountered.
 # The default value is: NO.
 
-WARN_AS_ERROR          = NO
+WARN_AS_ERROR          = YES
 
 # The WARN_FORMAT tag determines the format of the warning messages that doxygen
 # can produce. The string should contain the $file, $line, and $text tags, which
@@ -845,8 +845,7 @@ EXCLUDE_PATTERNS       =
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
 
-EXCLUDE_SYMBOLS        = std::* \
-                         Eigen::*
+EXCLUDE_SYMBOLS        =
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include

doxygen/doxygen.cfg

@@ -0,0 +1,11 @@
+[patterns]
+*.sh = LF
+*.MINPACK = CRLF
+scripts/*.in = LF
+debug/msvc/*.dat = CRLF
+debug/msvc/*.natvis = CRLF
+unsupported/test/mpreal/*.* = CRLF
+** = native
+
+[repository]
+native = LF

lib/eigen_3.3.3/unsupported/CMakeLists.txt

@@ -0,0 +1,34 @@
+syntax: glob
+qrc_*cxx
+*.orig
+*.pyc
+*.diff
+diff
+*.save
+save
+*.old
+*.gmo
+*.qm
+core
+core.*
+*.bak
+*~
+*build*
+*.moc.*
+*.moc
+ui_*
+CMakeCache.txt
+tags
+.*.swp
+activity.png
+*.out
+*.php*
+*.log
+*.orig
+*.rej
+log
+patch
+a
+a.*
+lapack/testing
+lapack/reference