roystgnr
diff --git a/.gitignore b/.gitignore
@@ -13,8 +13,9 @@ m4/ltversion.m4
 m4/lt~obsolete.m4
 src/Makefile.in
 test/Makefile.in
+test/run_unit_tests.sh
 *~
 build
 installed
-.clang-format
 TAGS
+.clang-format
diff --git a/CHANGES b/CHANGES
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,3 @@
-To see recent upstream changes, visit
+To see changes, run
 
- https://github.com/roystgnr/MetaPhysicL/commits/master
+$ git log
diff --git a/INSTALL b/INSTALL
@@ -1,8 +1,8 @@
 Installation Instructions
 *************************
 
-   Copyright (C) 1994-1996, 1999-2002, 2004-2016 Free Software
-Foundation, Inc.
+   Copyright (C) 1994-1996, 1999-2002, 2004-2017, 2020-2021 Free
+Software Foundation, Inc.
 
    Copying and distribution of this file, with or without modification,
 are permitted in any medium without royalty provided the copyright
@@ -225,7 +225,7 @@ order to use an ANSI C compiler:
 
 and if that doesn't work, install pre-built binaries of GCC for HP-UX.
 
-   HP-UX 'make' updates targets which have the same time stamps as their
+   HP-UX 'make' updates targets which have the same timestamps as their
 prerequisites, which makes it generally unusable when shipped generated
 files such as 'configure' are involved.  Use GNU 'make' instead.
 

diff --git a/Makefile.am b/Makefile.am
@@ -6,7 +6,7 @@ AUTOMAKE_OPTIONS = gnu
 ACLOCAL_AMFLAGS  = -I m4 -I m4/common -I m4/autoconf-submodule
 
 SUBDIRS          = src test doxygen
-EXTRA_DIST       = CHANGES LICENSE COPYING share docs
+EXTRA_DIST       = LICENSE COPYING share docs
 
 aclocaldir = $(prefix)/share/aclocal
 aclocal_DATA = $(top_srcdir)/share/aclocal/*

diff --git a/NEWS b/NEWS
@@ -1,3 +1,32 @@
+1.3.3 -> 1.4.0
+  * Throw exception in opt mode if DynamicStdArrayWrapper size exceeded
+  * Add tolerance argument to DynamicSparseNumberBase::sparsity_trim()
+  * ReplaceAlgebraicType metafunction
+  * ValueType overloads for std::array, std::vector
+  * MPI reduce support for DualNumber, SemiDynamicNumberArray, NumberArray
+  * More flexible assertion macros
+  * std::isinf overloads for DualNumber, DualExpression
+  * Unit testing with FP exceptions enabled
+  * Improved binary DualNumber operation speed + FPE safety
+  * Assorted bug fixes, compiler workarounds, unit tests, unit test fixes
+
+1.3.2 -> 1.3.3
+  * TIMPI configuration bugfix
+
+1.3.1 -> 1.3.2
+  * Unit test options for disabling long double tests
+  * Use SemiPermanent for derived StandardTypes
+  * Fix assertions in wrapper constructor/assignment
+  * --with-timpi-method configure option
+
+1.3.0 -> 1.3.1
+  * Build system fixes for "make check/distcheck" in some configurations
+
+1.2.2 -> 1.3.0
+  * StandardType specialization for SemiDynamicSparseNumberArray
+  * StandardType specialization for DynamicStdArrayWrapper
+  * Add template boolean parameter for StandardType and Packing of DualNumber
+
 1.2.1 -> 1.2.2
   * Restrict implicit conversions (fix for Eigen compatibility)
 

diff --git a/configure.ac b/configure.ac
@@ -2,10 +2,10 @@
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.61)
-AC_INIT(metaphysicl, 1.2.2, roystgnr@ices.utexas.edu)
+AC_INIT(metaphysicl, 1.4.0, roystgnr@ices.utexas.edu)
 AC_CONFIG_MACRO_DIR([m4])
 
-AC_CONFIG_HEADER(src/utilities/include/metaphysicl/metaphysicl_config.h.tmp)
+AC_CONFIG_HEADERS([src/utilities/include/metaphysicl/metaphysicl_config.h.tmp])
 dnl Prefixes everything in the temporary file with METAPHYSICL_
 AX_PREFIX_CONFIG_H(src/utilities/include/metaphysicl/metaphysicl_config.h,METAPHYSICL,src/utilities/include/metaphysicl/metaphysicl_config.h.tmp)
 
@@ -85,9 +85,30 @@ AM_CONDITIONAL(CXX14_ENABLED,test x$HAVE_CXX14 = x1)
 
 AM_CONDITIONAL(CXX11_ENABLED,test x$HAVE_CXX11 = x1)
 
+dnl Get CXXFLAGS and optional flags for this compiler
+ACSM_SET_CXX_FLAGS
+
+dnl Make sure it's safe to turn on FP exceptions
+ACSM_SET_FPE_SAFETY_FLAGS
+
+dnl provide the resulting flags to our Makefiles
+AC_SUBST(ACSM_CXXFLAGS_OPT)
+
+dnl Workaround for ACSM bug
+WERROR_FLAGS="$ACSM_WERROR_FLAGS"
+
 dnl -Wall warnings, -Wall the time.
 AX_CXXFLAGS_WARN_ALL
 
+dnl More warnings, for our own testing
+ACSM_ENABLE_PARANOID
+
+dnl And those tests should fail, not just whine
+ACSM_ENABLE_WERROR
+
+dnl See if we *can* turn on FP exceptions
+AC_HAVE_FEEXCEPT
+
 LT_INIT
 
 dnl---------------------------------------------------------
@@ -129,8 +150,9 @@ AS_IF([test "$enable_installed_timpi" = yes],
         HAVE_TIMPI_LIB=1
         AC_DEFINE(HAVE_TIMPI,1,[Define if TIMPI headers are available])
         AC_DEFINE(HAVE_TIMPI_LIB,1,[Define if a TIMPI library is available])
-        TIMPI_CPPFLAGS="-I$TIMPI_PREFIX/include $TIMPI_CPPFLAGS"
-        TIMPI_LIBS="-L$TIMPI_PREFIX/lib -ltimpi_opt $TIMPI_LIBS"
+        TIMPI_CPPFLAGS=""
+
+        TIMPI_LIBS="-ltimpi_$timpi_method"
       ],
       [])
 
@@ -203,6 +225,8 @@ AC_CONFIG_FILES([
   test/Makefile
   ])
 
+AC_CONFIG_FILES(test/run_unit_tests.sh, [chmod +x test/run_unit_tests.sh])
+
 # Must still call AC_OUTPUT() after generating all the files
 AC_OUTPUT()
 

diff --git a/m4/autoconf-submodule b/m4/autoconf-submodule
diff --git a/m4/common/acx_pthread.m4 b/m4/common/acx_pthread.m4
@@ -48,7 +48,7 @@ dnl @author Steven G. Johnson <stevenj@alum.mit.edu>
 AC_DEFUN([ACX_PTHREAD], [
 AC_REQUIRE([AC_CANONICAL_HOST])
 AC_LANG_SAVE
-AC_LANG_C
+AC_LANG([C])
 acx_pthread_ok=no
 
 # We used to check for pthread.h first, but this fails if pthread.h
@@ -162,13 +162,13 @@ for flag in $acx_pthread_flags; do
         # pthread_cleanup_push because it is one of the few pthread
         # functions on Solaris that doesn't have a non-functional libc stub.
         # We try pthread_create on general principles.
-        AC_TRY_LINK([#include <pthread.h>],
+        AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>],
                     [pthread_t th; pthread_join(th, (void**) 0);
                      pthread_attr_init((pthread_attr_t*) 0);
                      pthread_cleanup_push((void(*)(void *)) 0, (void*) 0);
                      pthread_create((pthread_t*) 0, (pthread_attr_t*) 0,
                                     (void*(*)(void *)) 0, (void*) 0);
-                     pthread_cleanup_pop(0); ],
+                     pthread_cleanup_pop(0); ])],
                     [acx_pthread_ok=yes])
 
         LIBS="$save_LIBS"
@@ -195,7 +195,7 @@ if test "x$acx_pthread_ok" = xyes; then
 	AC_MSG_CHECKING([for joinable pthread attribute])
 	attr_name=unknown
 	for attr in PTHREAD_CREATE_JOINABLE PTHREAD_CREATE_UNDETACHED; do
-	    AC_TRY_LINK([#include <pthread.h>], [int attr=$attr; return attr;],
+	    AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>], [int attr=$attr; return attr;])],
                         [attr_name=$attr; break])
 	done
         AC_MSG_RESULT($attr_name)

diff --git a/m4/common/ax_check_cl.m4 b/m4/common/ax_check_cl.m4
@@ -42,7 +42,7 @@ AC_REQUIRE([AC_PROG_SED])dnl
 AC_REQUIRE([ACX_PTHREAD])dnl
 
 AC_ARG_ENABLE([opencl],
-    [AC_HELP_STRING([--disable-opencl],
+    [AS_HELP_STRING([--disable-opencl],
                     [do not use OpenCL])],
     [enable_opencl=$enableval],
     [enable_opencl='yes'])
+74 −29		acsm_code_coverage.m4
+796 −0		acsm_compiler_flags.m4
+43 −0		acsm_enable_paranoid.m4
+34 −0		acsm_enable_werror.m4
+14 −14		acsm_mpi.m4
+1 −3		acsm_precision.m4
+8 −0		acsm_scrape_petsc_configure.m4
+74 −0		ax_check_compile_flag.m4
+9 −12		ax_subdirs_configure.m4