Merge branch 't/29702/move_all_code_from_src_setup_py__src_fpickle_se…

…tup_py_to_sage_setup' into t/29701/replace_use_of_module_list_optionalextension

build/bin/write-dockerfile.sh

@@ -158,7 +158,6 @@ $RUN ./bootstrap
 FROM bootstrapped as configured
 #:configuring:
 ADD src/bin src/bin
-ADD src/Makefile.in src/Makefile.in
 RUN mkdir -p logs/pkgs; ln -s logs/pkgs/config.log config.log
 ARG EXTRA_CONFIGURE_ARGS=""
 EOF

build/make/Makefile.in

@@ -85,14 +85,12 @@ STANDARD_PACKAGE_INSTS = \
 	$(foreach pkgname,$(STANDARD_PACKAGES),$(inst_$(pkgname)))
 
 # All optional installed packages (triggers the auto-update)
-OPTIONAL_INSTALLED_PACKAGES = \
-@SAGE_OPTIONAL_INSTALLED_PACKAGES@
+OPTIONAL_INSTALLED_PACKAGES = @SAGE_OPTIONAL_INSTALLED_PACKAGES@
 OPTIONAL_INSTALLED_PACKAGE_INSTS = \
     $(foreach pkgname,$(OPTIONAL_INSTALLED_PACKAGES),$(inst_$(pkgname)))
 
 # All previously installed optional packages that are to be uninstalled
-OPTIONAL_CLEANED_PACKAGES = \
-@SAGE_OPTIONAL_CLEANED_PACKAGES@
+OPTIONAL_CLEANED_PACKAGES = @SAGE_OPTIONAL_CLEANED_PACKAGES@
 OPTIONAL_CLEANED_PACKAGES_CLEANS = $(OPTIONAL_CLEANED_PACKAGES:%=%-clean)
 
 # All packages which should be downloaded
@@ -495,14 +493,14 @@ endif
 #
 # $(INST)/<pkgname>-<pkgvers>: <dependencies>
 #     $(AM_V_at)cd '$SAGE_ROOT' && \\
-#         source '$SAGE_ROOT/src/bin/sage-env' && \\
+#         . '$SAGE_ROOT/src/bin/sage-env' && \\
 #         sage-logger -p '$SAGE_ROOT/build/pkgs/<pkgname>/spkg-install' '$(SAGE_LOGS)/<pkgname>.log'
 #
 # <pkgname>: $(INST)/<pkgname>-<pkgvers>
 #
 # <pkgname>-clean:
 #     -$(AM_V_at)cd '$SAGE_ROOT' && \\
-#         source '$SAGE_ROOT/src/bin/sage-env' && \\
+#         . '$SAGE_ROOT/src/bin/sage-env' && \\
 #         '$SAGE_ROOT/build/pkgs/$PKG_NAME/spkg-uninstall'
 
 # Positional arguments:
@@ -513,16 +511,16 @@ define SCRIPT_PACKAGE_templ
 $(1)-build-deps: $(3)
 
 $$(INST)/$(1)-$(2): $(3)
-	$(AM_V_at)cd '$$(SAGE_ROOT)' && \
-		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
+	$(AM_V_at)cd '$$(SAGE_ROOT)/build/pkgs/$(1)' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && . '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log'
 	touch "$$@"
 
 $(1): $$(INST)/$(1)-$(2)
 
 $(1)-uninstall:
-	-$(AM_V_at)cd '$$(SAGE_ROOT)' && \
-		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
+	-$(AM_V_at)cd '$$(SAGE_ROOT)/build/pkgs/$(1)' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && . '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-uninstall'
 	-rm -f "$$(INST)/$(1)-$(2)"
 

build/pkgs/cvxopt/spkg-install.in

@@ -1,20 +1,69 @@
 cd src
 
-# Stolen from Gentoo
-pkg_libs() {
-	pkg-config --libs-only-l $* | \
-		sed -e 's:[ ]-l*\(pthread\|m\)\([ ]\|$\)::g' -e 's:[ ]*$::' | \
-		tr ' ' '\n' | sort -u | sed -e "s:^-l\(.*\):\1:g" | \
-		tr '\n' ';' | sed -e 's:;$::'
-}
+# This is a POSIX (non-bash) compatible version of the same function
+# in the Gentoo cvxopt package. It's more general than it needs to
+# be right now because we may need to use the "L" and "I" modes in
+# the future to support system installations of e.g. suitesparse.
+#
+# The BLAS_LIB and LAPACK_LIB variables (among others) in cvxopt's
+# setup.py are passed in as colon-delimited strings. So, for example,
+# if your blas "l" flags are "-lblas -lcblas", then cvxopt wants
+# "blas;cblas" for BLAS_LIB.
+#
+# The following function takes a flag type ("l", "L", or "I") as its
+# first argument and a list of packages as its remaining arguments. It
+# outputs a list of libraries, library paths, or include paths,
+# respectively, for the given packages, retrieved using pkg-config and
+# deduplicated, in the appropriate format.
+#
+cvxopt_output() {
+    FLAGNAME="${1}"
+    shift
+    PACKAGES="${@}"
+
+    case "${FLAGNAME}" in
+	l) PKGCONFIG_MODE="--libs-only-l";;
+	L) PKGCONFIG_MODE="--libs-only-L";;
+	I) PKGCONFIG_MODE="--cflags-only-I";;
+	*) echo "invalid flag name: ${FLAGNAME}"; exit 1;;
+    esac
+
+    CVXOPT_OUTPUT=""
+    for PKGCONFIG_ITEM in $(pkg-config ${PKGCONFIG_MODE} ${PACKAGES}); do
+	# First strip off the leading "-l", "-L", or "-I", and replace
+	# it with a semicolon...
+	PKGCONFIG_ITEM=";${PKGCONFIG_ITEM#-${FLAGNAME}}"
 
+	# Now check to see if this element is already present in the
+	# list, and skip it if it is. This eliminates multiple entries
+	# from winding up in the list when multiple package arguments are
+	# passed to this function.
+	if [ "${CVXOPT_OUTPUT}" != "${CVXOPT_OUTPUT%${PKGCONFIG_ITEM}}" ]
+	then
+	    # It was already the last entry in the list, so skip it.
+	    continue
+	elif [ "${CVXOPT_OUTPUT}" != "${CVXOPT_OUTPUT%${PKGCONFIG_ITEM};*}" ]
+	then
+	    # It was an earlier entry in the list. These two cases are
+	    # separate to ensure that we can e.g. find ";m" at the end
+	    # of the list, but that we don't find ";metis" in the process.
+	    continue
+	fi
+
+	# It isn't in the list yet, so append it.
+	CVXOPT_OUTPUT="${CVXOPT_OUTPUT}${PKGCONFIG_ITEM}"
+    done
+
+    # Strip the leading ";" from ";foo;bar" before output.
+    echo "${CVXOPT_OUTPUT#;}"
+}
 
 # configure cvxopt by variables
 # Note that *_INC_DIR variables have to be non-empty.
 # Compilers don't like "-I ".
-export CVXOPT_BLAS_LIB="$(pkg_libs blas)"
+export CVXOPT_BLAS_LIB="$(cvxopt_output l blas)"
 export CVXOPT_BLAS_LIB_DIR="$(pkg-config --variable=libdir blas)"
-export CVXOPT_LAPACK_LIB="$(pkg_libs lapack)"
+export CVXOPT_LAPACK_LIB="$(cvxopt_output l lapack)"
 
 if test "x$SAGE_SUITESPARSE_LOCALINSTALL" != "x"; then
    export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_LOCAL}"

build/pkgs/fflas_ffpack/patches/fix-ksh-pkgconfig.patch

@@ -0,0 +1,28 @@
+From 33a5ec4977f36ce3a24c9ee824d9dd053b8cea04 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dimpase@gmail.com>
+Date: Fri, 8 May 2020 15:55:27 +0100
+Subject: [PATCH 1/1] remove 1st and last file in .pc file
+
+this causes problem if building with ksh, as they remain, causing a broken .pc file.
+---
+ fflas-ffpack.pc.in | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/fflas-ffpack.pc.in b/fflas-ffpack.pc.in
+index a2618d6..e34a744 100644
+--- a/fflas-ffpack.pc.in
++++ b/fflas-ffpack.pc.in
+@@ -1,4 +1,3 @@
+-/------------------ fflas-ffpack.pc ------------------------
+ prefix=@prefix@
+ exec_prefix=@prefix@
+ libdir=@prefix@/lib
+@@ -11,4 +10,3 @@ Version: @VERSION@
+ Requires: givaro >= 4.0.3
+ Libs: @PARLIBS@ @PRECOMPILE_LIBS@ @BLAS_LIBS@
+ Cflags: -I@includedir@  @BLAS_CFLAGS@  @PARFLAGS@ @PRECOMPILE_FLAGS@ @REQUIRED_FLAGS@
+-\-------------------------------------------------------
+\ No newline at end of file
+-- 
+2.26.2
+

build/pkgs/givaro/patches/fix-ksh-pkgconfig.patch

@@ -0,0 +1,27 @@
+From 91dcba743e15288abe69966a5f71704d9adcc57c Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dimpase@gmail.com>
+Date: Fri, 8 May 2020 10:22:57 +0100
+Subject: [PATCH 1/1] remove 1st and last lines in givaro.pc.in
+
+---
+ givaro.pc.in | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/givaro.pc.in b/givaro.pc.in
+index 285b854..af38bf3 100644
+--- a/givaro.pc.in
++++ b/givaro.pc.in
+@@ -1,4 +1,3 @@
+-/------------------ givaro.pc ------------------------
+ prefix=@prefix@
+ exec_prefix=@prefix@
+ libdir=@prefix@/lib
+@@ -11,4 +10,3 @@ Version: @VERSION@
+ Requires:
+ Libs: -L@libdir@ -lgivaro @LIBS@
+ Cflags: -I@includedir@ @REQUIRED_FLAGS@
+-\-------------------------------------------------------
+\ No newline at end of file
+-- 
+2.26.2
+

build/pkgs/linbox/patches/fix-ksh-pkgconfig.patch

@@ -0,0 +1,28 @@
+From 52c78df67a08de074991a93b57946b7bd5ea7196 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dimpase@gmail.com>
+Date: Fri, 8 May 2020 15:53:25 +0100
+Subject: [PATCH 1/1] remove redundant 1st and last lines
+
+they remain if the script is run under ksh, leading to broken .pc file
+---
+ linbox.pc.in | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/linbox.pc.in b/linbox.pc.in
+index f54285e..eb6835b 100644
+--- a/linbox.pc.in
++++ b/linbox.pc.in
+@@ -1,4 +1,3 @@
+-/------------------ linbox.pc ------------------------
+ prefix=@prefix@
+ exec_prefix=@prefix@
+ libdir=@libdir@
+@@ -11,4 +10,4 @@ Version: @VERSION@
+ Requires: fflas-ffpack >= 2.4.0, givaro >= 4.1.0
+ Libs: -L${libdir} -llinbox @LINBOXSAGE_LIBS@ @NTL_LIBS@ @MPFR_LIBS@ @FPLLL_LIBS@ @IML_LIBS@ @FLINT_LIBS@ @OCL_LIBS@
+ Cflags: @DEFAULT_CFLAGS@ -DDISABLE_COMMENTATOR -I${includedir} @NTL_CFLAGS@ @MPFR_CFLAGS@ @FPLLL_CFLAGS@  @IML_CFLAGS@ @FLINT_CFLAGS@ 
+-\-------------------------------------------------------
++
+-- 
+2.26.2
+

build/pkgs/lrcalc/spkg-install.in

@@ -1,7 +1,8 @@
 cd src
 
 # Use newer version of config.guess and config.sub (see Trac #19725)
-cp "$SAGE_ROOT"/config/config.* .
+cp "$SAGE_ROOT"/config/config.guess .
+cp "$SAGE_ROOT"/config/config.sub .
 
 sdh_configure
 sdh_make

build/pkgs/mpc/spkg-configure.m4

@@ -8,7 +8,7 @@ SAGE_SPKG_CONFIGURE([mpc], [
         AC_MSG_RESULT([no])
         AC_CHECK_HEADER(mpc.h, [], [sage_spkg_install_mpc=yes])
         dnl mpc_cmp_abs appeared in MPC 1.1.0
-        AC_SEARCH_LIBS([mpc_cmp_abs], [mpc], [break], [sage_spkg_install_mpc=yes])
+        AC_SEARCH_LIBS([mpc_cmp_abs], [mpc], [], [sage_spkg_install_mpc=yes])
     fi
 ], [], [], [
     if test x$sage_spkg_install_mpc = xyes; then

build/pkgs/mpfr/spkg-configure.m4

@@ -8,7 +8,7 @@ SAGE_SPKG_CONFIGURE([mpfr], [
         AC_MSG_RESULT([no])
         AC_CHECK_HEADER(mpfr.h, [], [sage_spkg_install_mpfr=yes])
         dnl mpfr_free_pool appeared in r11922 (Dec 2017) on MPFR svn
-        AC_SEARCH_LIBS([mpfr_free_pool], [mpfr], [break], [sage_spkg_install_mpfr=yes])
+        AC_SEARCH_LIBS([mpfr_free_pool], [mpfr], [], [sage_spkg_install_mpfr=yes])
     fi
 ], [], [], [
     if test x$sage_spkg_install_mpfr = xyes; then

build/pkgs/mpir/spkg-configure.m4

@@ -5,7 +5,7 @@ dnl Implement cases for what to do on different options here
             AC_CHECK_HEADER(gmp.h, [], [sage_spkg_install_mpir=yes])
             AC_CHECK_HEADER(gmpxx.h, [], [sage_spkg_install_mpir=yes])
             dnl mpq_cmp_z appeared in GMP 6.1.0 and is used by pynac
-            AC_SEARCH_LIBS([__gmpq_cmp_z], [gmp], [break],
+            AC_SEARCH_LIBS([__gmpq_cmp_z], [gmp], [],
                 [sage_spkg_install_mpir=yes])
             SAGE_MP_LIBRARY=mpir
             ;;

build/pkgs/ncurses/spkg-configure.m4

@@ -2,8 +2,8 @@ SAGE_SPKG_CONFIGURE([ncurses], [
     dnl First try checking for ncurses with pkg-config
     PKG_CHECK_MODULES([NCURSES], [ncurses >= 6.0], [],
       [AC_CHECK_HEADERS([ncurses.h],
-        [AC_SEARCH_LIBS([wresize], [ncurses tinfo], [break],
-                       [sage_spkg_install_ncurses=yes])], 
+        [AC_SEARCH_LIBS([wresize], [ncurses tinfo], [],
+                       [sage_spkg_install_ncurses=yes])],
         [sage_spkg_install_ncurses=yes])],
       [sage_spkg_install_ncurses=yes])
 ])

build/pkgs/readline/spkg-configure.m4

@@ -11,7 +11,7 @@ SAGE_SPKG_CONFIGURE([readline], [
       [AC_CHECK_HEADERS([readline/readline.h],
   dnl rl_bind_keyseq is not present in macos's readline
   dnl and is not present in readline version 4 (the one in OpenBSD)
-        [AC_SEARCH_LIBS([rl_bind_keyseq], [readline], [break],
+        [AC_SEARCH_LIBS([rl_bind_keyseq], [readline], [],
                         [sage_spkg_install_readline=yes])],
         [sage_spkg_install_readline=yes])],
       [sage_spkg_install_readline=yes])

build/pkgs/sage_conf/spkg-install

@@ -9,4 +9,4 @@ if [ $? -ne 0 ]; then
     echo >&2 "Is $SAGE_ROOT the correct SAGE_ROOT?"
     exit 1
 fi
-cd $SAGE_ROOT/build/pkgs/sage_conf/src && sdh_pip_install .
+cd src && sdh_pip_install .

build/pkgs/texlive/spkg-install

@@ -1 +1 @@
-exec sage-python23 build/pkgs/texlive/spkg-install.py
+exec sage-python23 spkg-install.py

configure.ac

@@ -28,31 +28,6 @@ AC_PREREQ([2.69])
 AC_DEFUN([SAGE_VERSION], m4_esyscmd_s([. src/bin/sage-version.sh && echo $SAGE_VERSION]))
 AC_INIT([Sage], SAGE_VERSION, [sage-devel@googlegroups.com])
 
-# The following needs to be immediately after calling AC_INIT
-#------------------------------------------------------------
-# We need to run this configure script with bash
-if test -z "$BASH_VERSION"
-then
-    CONFIG_SHELL=`command -v bash`
-    export CONFIG_SHELL
-    if $CONFIG_SHELL -c "exit 0"
-    then
-        exec $CONFIG_SHELL $0 "$@"
-    else
-        AC_MSG_NOTICE([The 'bash' shell is needed to build AC_PACKAGE_NAME])
-        AC_MSG_NOTICE([All modern systems will have the 'bash' shell installed somewhere])
-        if test -d /opt/OpenSource/bin
-        then
-           AC_MSG_NOTICE([On HP-UX you may try adding /opt/OpenSource/bin to your path])
-        fi
-        if test -d /opt/pware/bin
-        then
-           AC_MSG_NOTICE([On AIX you may try adding /opt/pware/bin to your path])
-        fi
-        AC_MSG_ERROR(['bash' not found])
-    fi
-fi
-
 
 AC_COPYRIGHT([GPL version 3])
 AC_CONFIG_SRCDIR([configure.ac])
@@ -447,13 +422,12 @@ SAGE_SPKG_COLLECT()
 # TODO: fix this in Trac #21524
 touch "$SAGE_SRC/bin/sage-env-config"
 
-SAGE_SCRIPTS='\
-'
+SAGE_SCRIPTS=''
 for file in "$SAGE_SRC/bin/"*; do
     # Skip files with ".in" extension
     ext=${file##*.}
     if test "$ext" != in; then
-        SAGE_SCRIPTS+="    \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"$'\n'
+        SAGE_SCRIPTS="${SAGE_SCRIPTS} \\$(printf '\n    ')\$(SAGE_LOCAL)${file#$SAGE_SRC}"
     fi
 done