Bump factory to 4.4.1 and FLINT to 3.2.1

.gitmodules

@@ -12,7 +12,7 @@
 	url = https://github.com/Macaulay2/bdwgc.git
 [submodule "M2/submodules/flint"]
 	path = M2/submodules/flint
-	url = https://github.com/Macaulay2/flint2.git
+	url = https://github.com/flintlib/flint
 [submodule "M2/submodules/frobby"]
 	path = M2/submodules/frobby
 	url = https://github.com/Macaulay2/frobby.git

M2/Macaulay2/e/NCAlgebras/FreeAlgebra.hpp

@@ -9,7 +9,6 @@
 #include "ringelem.hpp"               // for ring_elem
 #include "style.hpp"                  // for GEOHEAP_SIZE
 
-#include <gmp.h>                      // for mpz_srcptr, mpq_srcptr
 #include <iosfwd>                     // for ostream, string
 #include <utility>                    // for pair
 #include <vector>                     // for vector

M2/Macaulay2/e/NCAlgebras/FreeAlgebraQuotient.hpp

@@ -8,7 +8,6 @@
 #include "newdelete.hpp"              // for our_new_delete
 #include "ringelem.hpp"               // for ring_elem
 
-#include <gmp.h>                      // for mpz_srcptr, mpq_srcptr
 #include <vector>                     // for vector
 
 class Ring;

M2/Macaulay2/e/aring-gf-flint-big.hpp

@@ -8,6 +8,9 @@
 // The following needs to be included before any flint files are included.
 #include <M2/gc-include.h>
 
+// includes gmp.h, which is required for FLINT functions that use GMP
+#include <M2/math-include.h>
+
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wconversion"
 #include <flint/flint.h>       // for flint_free, flint_rand_t, fmpz_t

M2/Macaulay2/e/aring-gf-flint.hpp

@@ -8,6 +8,9 @@
 // The following needs to be included before any flint files are included.
 #include <M2/gc-include.h>
 
+// includes gmp.h, which is required for FLINT functions that use GMP
+#include <M2/math-include.h>
+
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wconversion"
 #include <flint/flint.h>      // for flint_rand_t, fmpz_t, ulong

M2/Macaulay2/e/schreyer-resolution/res-f4-m2-interface.cpp

@@ -33,7 +33,6 @@
 #include "schreyer-resolution/res-schreyer-frame.hpp"     // for SchreyerFrame
 #include "schreyer-resolution/res-schreyer-order.hpp"     // for ResSchreyer...
 #include "timing.hpp"                                     // for timer, seconds
-#include <gmp.h>                                          // for mpz_clear
 #include <cstdlib>                                        // for exit, size_t
 #include <chrono>                                         // for common_type...
 #include <iostream>                                       // for operator<<

M2/Macaulay2/m2/programs.m2

@@ -89,18 +89,21 @@ findProgram(String, List) := opts -> (name, cmds) -> (
 	instance(opts.MinimumVersion, Sequence) and
 	class \ opts.MinimumVersion === (String, String)) then
 	error "expected MinimumVersion to be a sequence of two strings";
-    pathsToTry := fixPath \ join(
+    pathsToTry := fixPath \ nonnull flatten {
 	-- try user-configured path first
-	if programPaths#?name then {programPaths#name} else {},
+	if programPaths#?name then programPaths#name,
 	-- now try M2-installed path
-	{prefixDirectory | currentLayout#"programs"},
+	prefixDirectory | currentLayout#"programs",
 	-- any additional paths specified by the caller
-	opts.AdditionalPaths,
+	 opts.AdditionalPaths,
 	-- try PATH
-	if getenv "PATH" == "" then {} else apply(separate(":", getenv "PATH"),
+	if getenv "PATH" =!= "" then apply(
+	    separate(":", getenv "PATH"),
 	    dir -> if dir == "" then "." else dir),
 	-- try directory containing M2-binary
-	{bindir});
+	bindir,
+	-- try usr-host/bin
+	if topBuilddir =!= null then topBuilddir | "usr-host/bin"};
     prefixes := {(".*", "")} | opts.Prefix;
     errorCode := didNotFindProgram;
     versionFound := "0.0";

M2/Macaulay2/m2/startup.m2.in

@@ -40,7 +40,6 @@ if not firstTime then debug Core -- we need access to the private symbols (we re
 toString := value' getGlobalSymbol if firstTime then "simpleToString" else "toString"
 
 local exe
-local topBuilddir
 
 -- this next bit has to be *parsed* after the "debug" above, to prevent the symbols from being added to the User dictionary
 if firstTime then (

M2/Macaulay2/packages/Macaulay2Doc/ov_preface.m2

@@ -344,10 +344,8 @@ document {
      G.-M. Greuel, R. Stobbe, G. Pfister, H. Schoenemann, and J. Schmidt,
      University of Kaiserslautern, Macaulay2 incorporates ", TT "Singular-Factory", ",
      version ", version#"factory version", ", a free library of polynomial routines
-     that provides for factorization of polynomials.  It is available at 
-     ", HREF "ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory"," and at 
-     ", HREF "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES", ".  It
-     is part of ", TT "Singular", ", whose home page is ", HREF "http://www.singular.uni-kl.de/", ".",
+     that provides for factorization of polynomials.  It is part of ",
+     TT "Singular", ", whose home page is ", HREF "https://www.singular.uni-kl.de/", ".",
      PARA{},
      "The following important routines call upon it:",
      UL {

M2/check-configure/Makefile.in

@@ -18,7 +18,8 @@ check-config:
 	    @abs_top_srcdir@/configure						\
 	    PKG_CONFIG_PATH=$(BUILTLIBPATH)/lib/pkgconfig:$(PKG_CONFIG_PATH)	\
 	    GFTABLESDIR=@PRE_GFTABLESDIR@					\
-	    LDFLAGS="@BUILTLIBS@ $(LDFLAGS)"					\
+	    LDFLAGS="$(LDFLAGS)"						\
+	    LIBS="@BUILTLIBS@"							\
 	    --with-gtest-source-path="@GTEST_PATH@"				\
 	    CPPFLAGS="$(CPPFLAGS)"						\
 	    CC="$(CC)"								\

M2/cmake/build-libraries.cmake

@@ -343,25 +343,26 @@ _ADD_COMPONENT_DEPENDENCY(libraries ntl gmp NTL_FOUND)
 ExternalProject_Add(build-flint
   PREFIX            libraries/flint
   SOURCE_DIR        ${CMAKE_SOURCE_DIR}/submodules/flint
-  BINARY_DIR        libraries/flint/build
-  CMAKE_ARGS        -DCMAKE_INSTALL_PREFIX=${M2_HOST_PREFIX}
-                    -DCMAKE_SYSTEM_PREFIX_PATH=${M2_HOST_PREFIX}
-                    -DCMAKE_MODULE_PATH=${CMAKE_SOURCE_DIR}/cmake
-                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-                    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-                    -DCMAKE_C_FLAGS=${CFLAGS}
-                    -DCMAKE_CXX_FLAGS=${CXXFLAGS}
-                    -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
-                    -DIPO_SUPPORTED=OFF # TODO: because of clang; see https://github.com/wbhart/flint2/issues/644
-                    -DWITH_NTL=ON
-  INSTALL_COMMAND   ${CMAKE_COMMAND} --install . ${strip_setting}
+  BUILD_IN_SOURCE   ON
+  CONFIGURE_COMMAND ./bootstrap.sh &&
+                    ${CONFIGURE} --prefix=${M2_HOST_PREFIX}
+                    ${shared_setting}
+                    "CPPFLAGS=${CPPFLAGS} -I${GMP_INCLUDE_DIRS}"
+                    CFLAGS=${CFLAGS}
+                    CXXFLAGS=${CXXFLAGS}
+                    "LDFLAGS=${LDFLAGS} -L${GMP_LIBRARY_DIRS}"
+                    CC=${CMAKE_C_COMPILER}
+                    CXX=${CMAKE_CXX_COMPILER}
+                    AR=${CMAKE_AR}
+                    OBJDUMP=${CMAKE_OBJDUMP}
+                    STRIP=${CMAKE_STRIP}
+                    RANLIB=${CMAKE_RANLIB}
+  BUILD_COMMAND     ${MAKE} -j${PARALLEL_JOBS}
+  INSTALL_COMMAND   ${MAKE} -j${PARALLEL_JOBS} install
           COMMAND   ${CMAKE_COMMAND} -E make_directory ${M2_INSTALL_LICENSESDIR}/flint
           COMMAND   ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/submodules/flint/README.md ${M2_INSTALL_LICENSESDIR}/flint
-          COMMAND   ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/submodules/flint/LICENSE ${M2_INSTALL_LICENSESDIR}/flint
-  TEST_COMMAND      ${CMAKE_COMMAND} . -DBUILD_TESTING=ON
-       COMMAND      ${CMAKE_COMMAND} --build .
-       COMMAND      ${CMAKE_COMMAND} --build . --target test
+          COMMAND   ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/submodules/flint/COPYING ${M2_INSTALL_LICENSESDIR}/flint
+  TEST_COMMAND      ${MAKE} -j${PARALLEL_JOBS} check
   EXCLUDE_FROM_ALL  ON
   TEST_EXCLUDE_FROM_MAIN ON
   STEP_TARGETS      install test
@@ -376,8 +377,8 @@ _ADD_COMPONENT_DEPENDENCY(libraries flint "gmp;mpfr;ntl" FLINT_FOUND)
 # https://service.mathematik.uni-kl.de/ftp/pub/Math/Singular/Factory/
 # TODO: what is ftmpl_inst.o?
 ExternalProject_Add(build-factory
-  URL               https://www.singular.uni-kl.de/ftp/pub/Math/Factory/factory-4.4.0.tar.gz
-  URL_HASH          SHA256=baf31159578463e26bf18ec68ec901228d79a819866dd96c02d85c73dfbaf030
+  URL               https://macaulay2.com/Downloads/OtherSourceCode/factory-4.4.1.tar.gz
+  URL_HASH          SHA256=345ec8ab2481135d18244e2a2ff6bc16e812a39a9eb5ac5d578956d8e0526e6e
   PREFIX            libraries/factory
   SOURCE_DIR        libraries/factory/build
   DOWNLOAD_DIR      ${CMAKE_SOURCE_DIR}/BUILD/tarfiles

M2/configure.ac

@@ -615,7 +615,7 @@ AC_SUBST(BUILTLIBS)
 AC_SUBST(LIBLIST, " gc gdbm gmp mpfr mpfi normaliz readline ntl flint factory lapack mpsolve frobby glpk cddlib fplll givaro fflas_ffpack linbox gtest tbb memtailor mathic mathicgb eigen ")
 # The list LIBLIST is the list of libraries that might be used and linked into M2.
 
-AC_SUBST(PROGLIST, "4ti2 gfan csdp nauty cddplus lrslib gftables topcom cohomcalg msolve")
+AC_SUBST(PROGLIST, "4ti2 gfan csdp nauty cddplus lrslib topcom cohomcalg msolve")
 # The list PROGLIST is the list of programs and libraries for them that are distributed with M2.
 #     Initially, we offer no option for not compiling some of them.
 
@@ -678,7 +678,7 @@ PKGNAME_fflas_ffpack=fflas-ffpack
 #############################################################################
 
 LIBLIST=" $LIBLIST "
-AC_ARG_ENABLE(build-libraries, AS_HELP_STRING(--enable-build-libraries=...,[list of libraries and programs to build from downloaded source code (e.g., gc gdbm mpfr mpfi readline ntl gftables factory lapack mpsolve frobby glpk cddlib givaro fflas_ffpack linbox 4ti2 gfan normaliz csdp nauty cddplus lrslib msolve)]),
+AC_ARG_ENABLE(build-libraries, AS_HELP_STRING(--enable-build-libraries=...,[list of libraries and programs to build from downloaded source code (e.g., gc gdbm mpfr mpfi readline ntl factory lapack mpsolve frobby glpk cddlib givaro fflas_ffpack linbox 4ti2 gfan normaliz csdp nauty cddplus lrslib msolve)]),
     [for i in $enableval
      do case " $LIBLIST $PROGLIST " in
 	    *" $i "*) 
@@ -1490,10 +1490,8 @@ AC_ARG_VAR([GFTABLESDIR],
     [path to gftables directory if factory is already installed])
 if test $BUILD_factory = yes
 then
-    BUILD_gftables=yes
     GFTABLESDIR="${datadir}/Macaulay2/Core/factory/"
 else
-    BUILD_gftables=no
     if test x$GFTABLESDIR = x
     then
 	if test $FACTORY_NAME = factory
@@ -1969,7 +1967,7 @@ done
 prefix=$save_prefix
 exec_prefix=$save_exec_prefix
 
-if test $BUILD_gftables = no
+if test $BUILD_factory = no
 then PRE_GFTABLESDIR="$GFTABLESDIR"
 else
 PRE_GFTABLESDIR="$pre_datadir/Macaulay2/Core/factory/"

M2/libraries/factory/Makefile.in

@@ -1,22 +1,11 @@
-# https://www.singular.uni-kl.de/
-# svn co svn+ssh://monty.mathematik.uni-kl.de/usr/local/Singular/svn/trunk
-# svn co http://www.singular.uni-kl.de/svn/trunk
-# old URL = ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory
-# URL = ftp://jim.mathematik.uni-kl.de/pub/Math/Factory
-# https://github.com/Singular/Sources
-# https://service.mathematik.uni-kl.de/ftp/pub/Math/Factory/factory-4.2.0.tar.gz
-# ftp://jim.mathemathematik.uni-kl.de/pub/Math/Singular
-# https://www.singular.uni-kl.de
-# https://www.singular.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-3-0/singular-4.3.0.tar.gz
-
-# We seem to be the only users of the factory library, which is part of
-# Singular.  Its source code accompanies binary installations of Singular,
-# under Arch Linux, for example.  To get a more recent tar file for factory,
-# I ask Hans Schoenemann <hannes@mathematik.uni-kl.de> to make one and post
-# it at one of the ftp sites above.  Version 4.1.3 is available.
-
-URL = https://www.singular.uni-kl.de/ftp/pub/Math/Factory
-VERSION = 4.4.0
+# The Singular developers no longer publish a factory tarball on their
+# website, so we generate our own.  To do so, run:
+# make -C libraries/factory dist
+# This will generate a tarball in BUILD/tarfiles
+# Upload this to https://macaulay2.com/Downloads/OtherSourceCode/
+
+URL = https://macaulay2.com/Downloads/OtherSourceCode
+VERSION = 4.4.1
 #PATCHFILE = @abs_srcdir@/patch-$(VERSION)
 PRECONFIGURE = autoreconf -vif
 
@@ -48,6 +37,7 @@ CONFIGOPTIONS += --disable-omalloc --enable-streamio
 CONFIGOPTIONS += --includedir='$(LIBRARIESDIR)/include/'
 CONFIGOPTIONS += --disable-shared
 CONFIGOPTIONS += --without-Singular
+CONFIGOPTIONS += --datadir=@pre_packagesdir@/Core # for gftables
 
 ifeq (@DEBUG@,yes)
 CONFIGOPTIONS += --enable-assertions 
@@ -100,6 +90,17 @@ uninstall clean ::
 		include/factory.h include/factoryconf.h include/cf_gmp.h include/templates/ftmpl_* include/factory ; \
 	fi
 
+dist:
+	rm -rf Singular
+	@GIT@ clone https://github.com/Singular/Singular --single-branch \
+		-b Release-$(subst .,-,$(VERSION)) --depth=1
+# Remove if https://github.com/Singular/Singular/pull/1265 merged
+	sed -i 's/make dist/.\/configure \&\& make dist/' \
+		Singular/factory/make_factory_dist
+	cd Singular/factory && sh make_factory_dist
+	cp Singular/factory/factory-$(VERSION).tar.gz $(TARFILE_DIR)
+	rm -rf Singular
+
 #post-install: $(LIBRARIESDIR)/lib/libcfmem-newdelete-removed
 #$(LIBRARIESDIR)/lib/libcfmem-newdelete-removed : $(LIBRARIESDIR)/lib/libcfmem.a
 #	ar -d "$^" newdelete.o

M2/libraries/flint/Makefile.in

@@ -2,14 +2,14 @@ SUBMODULE = true
 # LIBNAME = flint2
 HOMEPAGE = http://flintlib.org
 # git://github.com/wbhart/flint2.git
-VERSION = 3.0.0
+VERSION = 3.2.1
 # PATCHFILE = @abs_srcdir@/patch-$(VERSION)
 PARALLEL = yes
 
 # Many other tests keep failing, so disable them all:
 CHECKTARGET = .
 
-LICENSEFILES = LICENSE
+LICENSEFILES = COPYING
 ifeq (@DEBUG@,yes)
 CONFIGOPTIONS += --enable-assert
 CFLAGS += -O0 -fno-unroll-loops 

M2/m4/files

@@ -42,7 +42,6 @@ libraries/frobby/Makefile
 libraries/gc/Makefile
 libraries/gdbm/Makefile
 libraries/gfan/Makefile
-libraries/gftables/Makefile
 libraries/givaro/Makefile
 libraries/glpk/Makefile
 libraries/gmp/Makefile