Merge tag '9.1.beta6' into t/29041/at___bootstrap_time__generate_src_…

…requirements_txt__src_constraints_txt__src_setup_cfg__install_requires__from_build_pkgs

SageMath version 9.1.beta6, Release Date: 2020-03-01

.gitignore

@@ -90,3 +90,5 @@ Untitled*.ipynb
 # GitLab CI generated files #
 #############################
 gitlab-build-docker.log
+
+/build/bin/sage-build-env-config

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta5, Release Date: 2020-02-21
+SageMath version 9.1.beta6, Release Date: 2020-03-01

build/bin/sage-build-env-config.in

@@ -0,0 +1,87 @@
+# -*- shell-script -*-
+
+###########################################################################
+#
+#  Set some environment variables for building Sage (the distribution).
+#
+#  NOTES:
+#  - You must *source* this script instead of executing.
+#  - Use "return" instead of "exit" to signal a failure.  Since this
+#    file is sourced, an "exit" here will actually exit src/bin/sage,
+#    which is probably not intended.
+#  - All environment variables set here should be *exported*, otherwise
+#    they won't be available in child programs.
+#
+#  If you want to set all environment variables for your shell like
+#  they are during the build of Sage packages, type
+#
+#             sage --buildsh
+#
+##########################################################################
+
+# This is usually blank if the system GMP is used, or $SAGE_LOCAL otherwise
+export SAGE_GMP_PREFIX="@SAGE_GMP_PREFIX@"
+export SAGE_GMP_INCLUDE="@SAGE_GMP_INCLUDE@"
+if [ -n "$SAGE_GMP_PREFIX" ]; then
+    # Many packages that depend on GMP accept a --with-gmp=<prefix> flag to
+    # their ./configure scripts.  When using the system's GMP this is not
+    # generally necessary, but when using the GMP package installed in
+    # SAGE_LOCAL it is useful to pass it.  We define this variable to
+    # pass to these packages' ./configure scripts.  When using the system
+    # GMP its value is just blank (for many of these packages passing
+    # --with-gmp without an argument is actually a bug)
+    export SAGE_CONFIGURE_GMP="--with-gmp=$SAGE_GMP_PREFIX"
+fi
+
+# The MPFR case is very close to the GMP case above
+# This is usually blank if the system MPFR is used, or $SAGE_LOCAL otherwise
+export SAGE_MPFR_PREFIX="@SAGE_MPFR_PREFIX@"
+if [ -n "$SAGE_MPFR_PREFIX" ]; then
+    # Some packages that depend on MPFR accept a --with-mpfr=<prefix> flag to
+    # their ./configure scripts. Thus we deal with this just as with GMP above. 
+    export SAGE_CONFIGURE_MPFR="--with-mpfr=$SAGE_MPFR_PREFIX"
+fi
+
+# The MPC case is very close to the MPFR case above
+# This is usually blank if the system MPC is used, or $SAGE_LOCAL otherwise
+export SAGE_MPC_PREFIX="@SAGE_MPC_PREFIX@"
+if [ -n "$SAGE_MPC_PREFIX" ]; then
+    # Some packages that depend on MPC accept a --with-mpc=<prefix> flag to
+    # their ./configure scripts. Thus we deal with this just as with GMP above. 
+    export SAGE_CONFIGURE_MPC="--with-mpc=$SAGE_MPC_PREFIX"
+fi
+
+# Location of system crti.o, in case we build our own gcc
+export SAGE_CRTI_DIR="@SAGE_CRTI_DIR@"
+
+# This is usually blank if the system NTL is used, or $SAGE_LOCAL otherwise
+export SAGE_NTL_PREFIX="@SAGE_NTL_PREFIX@"
+if [ -n "$SAGE_NTL_PREFIX" ]; then
+    # Many packages that depend on NTL accept a --with-ntl=<prefix> flag to
+    # their ./configure scripts.  When using the system's NTL this is not
+    # generally necessary, but when using the NTL package installed in
+    # SAGE_LOCAL it is useful to pass it.
+    export SAGE_CONFIGURE_NTL="--with-ntl=$SAGE_NTL_PREFIX"
+fi
+
+# The FLINT case is very close to the MPFR case above
+# This is usually blank if the system FLINT is used, or $SAGE_LOCAL otherwise
+export SAGE_FLINT_PREFIX="@SAGE_FLINT_PREFIX@"
+if [ -n "$SAGE_FLINT_PREFIX" ]; then
+    # Some packages that depend on FLINT accept a --with-flint=<prefix> flag to
+    # their ./configure scripts. Thus we deal with this just as with GMP above.
+    export SAGE_CONFIGURE_FLINT="--with-flint=$SAGE_FLINT_PREFIX"
+fi
+
+# This is usually blank if the system PARI is used, or $SAGE_LOCAL otherwise
+export SAGE_PARI_PREFIX="@SAGE_PARI_PREFIX@"
+if [ -n "$SAGE_PARI_PREFIX" ]; then
+    # Some packages that depend on PARI accept a --with-pari=<prefix> flag to
+    # their ./configure scripts. Thus we deal with this just as with GMP above.
+    export SAGE_CONFIGURE_PARI="--with-pari=$SAGE_PARI_PREFIX"
+fi
+export SAGE_PARI_CFG="@SAGE_PARI_CFG@"
+
+export SAGE_GLPK_PREFIX="@SAGE_GLPK_PREFIX@"
+export SAGE_FREETYPE_PREFIX="@SAGE_FREETYPE_PREFIX@"
+export SAGE_ARB_LIBRARY="@SAGE_ARB_LIBRARY@"

build/bin/sage-logger

@@ -77,7 +77,9 @@ if [ -n "$SAGE_SILENT_BUILD" -a ${use_prefix} = true ]; then
     ( exec>> $logfile 2>&1 ; eval "$cmd" )
     status=$?
     if [[ $status != 0 ]]; then
-        echo "  [$logname] error installing, exit status $status. Log file: $logfile"
+        echo "  [$logname] error installing, exit status $status. End of log file:"
+        tail -n 40 "$logfile" | sed "/Please email sage-devel/,$ d;s;^;  [$logname]   ;" >&2
+        echo "  [$logname] Full log file: $logfile"
     else
         echo "  [$logname] successfully installed."
     fi

build/bin/sage-spkg

@@ -723,7 +723,7 @@ export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"
 export PKG_VER="$PKG_VER"
 
-for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env" ; do
+for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env" "\$SAGE_ROOT/build/bin/sage-build-env-config"; do
     source "\$lib"
     if [ \$? -ne 0 ]; then
         echo >&2 "Error: failed to source \$lib"

build/make/Makefile.in

@@ -82,8 +82,6 @@ SDIST_PACKAGES = @SAGE_SDIST_PACKAGES@
 
 SCRIPTS = @SAGE_SCRIPTS@
 
-EXTCODE = @SAGE_EXTCODE@
-
 # Packages that use the 'normal' build rules
 NORMAL_PACKAGES = @SAGE_NORMAL_PACKAGES@
 
@@ -267,12 +265,12 @@ endif
 define SCRIPT_PACKAGE_templ
 $(1): $(2)
 	$(AM_V_at)cd '$$(SAGE_ROOT)' && \
-		source '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1).log'
 
 $(1)-clean:
 	-$(AM_V_at)cd '$$(SAGE_ROOT)' && \
-		source '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-uninstall'
 
 endef

build/make/deps

@@ -54,7 +54,6 @@ all-sage: \
 		$(STANDARD_PACKAGE_INSTS) \
 		$(OPTIONAL_INSTALLED_PACKAGE_INSTS) \
                 $(OPTIONAL_CLEANED_PACKAGES_CLEANS) \
-		$(EXTCODE) \
 		$(SCRIPTS)
 
 # Download all packages which should be inside an sdist tarball (the -B
@@ -124,6 +123,7 @@ base: $(inst_patch) $(inst_pkgconf)
 # Sage library (e.g. CYTHON, JINJA2), and on the other hand all
 # dependencies for Cython files (e.g. PARI, NTL, MP_LIBRARY).
 sagelib: \
+		$(SCRIPTS) \
 		$(inst_arb) \
 		$(inst_boost_cropped) \
 		$(inst_$(BLAS)) \
@@ -176,36 +176,26 @@ sagelib: \
 		$(inst_six) \
 		$(inst_symmetrica) \
 		$(inst_zn_poly) \
-		$(EXTCODE) \
 		$(PCFILES)
 	$(AM_V_at)if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
-		cd $(SAGE_SRC) && source bin/sage-env && \
+		cd $(SAGE_SRC) && source bin/sage-env && source $(SAGE_ROOT)/build/bin/sage-build-env-config && \
 		sage-logger -p 'time $(MAKE) sage' '$(SAGE_LOGS)/sagelib-$(SAGE_VERSION).log'; \
 	fi
 
 
 ###############################################################################
-# Building scripts and extcode
+# Building scripts
 ###############################################################################
 
 # Don't just use "install" since we don't want to change permissions
 $(SAGE_LOCAL)/bin/%: $(SAGE_SRC)/bin/%
 	$(AM_V_at)cp $< $@
 
-# Don't just use "install -D" since we don't want to change permissions.
-# cp won't correctly setup the SAGE_EXTCODE directory structure
-# (unlike install), so we need a mkdir here such that cp can copy into
-# an existing folder.
-$(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
-	@mkdir -p "$(@D)"
-	$(AM_V_at)cp $< $@
-
 # Install sage-specific generated .pc files
 $(SAGE_PKGCONFIG)/%.pc: $(SAGE_SRC)/lib/pkgconfig/%.pc
 	@mkdir -p "$(@D)"
 	$(AM_V_at)cp -P $< $@
 
-
 ###############################################################################
 # Building the documentation
 ###############################################################################

build/make/install

@@ -16,7 +16,6 @@ if [ $? -ne 0 ]; then
 fi
 
 export SAGE_SHARE="$SAGE_LOCAL/share"
-export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
 export SAGE_PKGCONFIG="$SAGE_LOCAL/lib/pkgconfig"
 export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
 export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"

build/pkgs/arb/patches/silence-stderr-exponent-too-large.patch

@@ -0,0 +1,37 @@
+Do not write stuff to stderr when signalling errors
+
+See https://trac.sagemath.org/ticket/28817
+
+
+diff --git a/arf/get_mpfr.c b/arf/get_mpfr.c
+index 34012af..9ccb87b 100644
+--- a/arf/get_mpfr.c
++++ b/arf/get_mpfr.c
+@@ -30,7 +30,6 @@ arf_get_mpfr(mpfr_t x, const arf_t y, mpfr_rnd_t rnd)
+     }
+     else if (COEFF_IS_MPZ(*ARF_EXPREF(y)))
+     {
+-        flint_printf("exception: exponent too large to convert to mpfr");
+         flint_abort();
+         r = 0; /* dummy return because flint_abort() is not declared noreturn */
+     }
+diff --git a/fmpr/get_mpfr.c b/fmpr/get_mpfr.c
+index 63b6682..e2dda3b 100644
+--- a/fmpr/get_mpfr.c
++++ b/fmpr/get_mpfr.c
+@@ -25,7 +25,6 @@ fmpr_get_mpfr(mpfr_t x, const fmpr_t y, mpfr_rnd_t rnd)
+     }
+     else if (COEFF_IS_MPZ(*fmpr_expref(y)))
+     {
+-        flint_printf("exception: exponent too large to convert to mpfr");
+         flint_abort();
+         r = 0; /* dummy return because flint_abort() is not declared noreturn */
+     }
+@@ -42,7 +41,6 @@ fmpr_get_mpfr(mpfr_t x, const fmpr_t y, mpfr_rnd_t rnd)
+
+         if (!mpfr_regular_p(x))
+         {
+-            flint_printf("exception: exponent too large to convert to mpfr");
+             flint_abort();
+         }
+     }

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c5ac16fd484b7d261fdd5f9ddc0ad144d212c074
-md5=6e01232385ed6a22fae6873990ca2b9a
-cksum=45471057
+sha1=63dd5a30099d2285ba7d8914dc6a94213e704258
+md5=767a51cc156fec7e49d08cbaefc38d24
+cksum=1354891695

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-f363300209b159a65d9ceaf6b79bb684a9c71db1
+30cb9d11bc3889744a2a27db00041d9cb40df522

build/pkgs/python3/spkg-build

@@ -107,7 +107,7 @@ fi
 
 echo "Testing importing of various modules..."
 import_errors=false
-test_modules="ctypes math hashlib crypt readline socket"
+test_modules="ctypes math hashlib crypt readline socket zlib sqlite3"
 if [ "$UNAME" = "Darwin" ]; then
     test_modules="$test_modules _scproxy"
 fi

configure.ac

@@ -433,21 +433,13 @@ done
 
 AC_SUBST([SAGE_SCRIPTS])
 
-SAGE_EXTCODE='\
-'
-for file in `find "$SAGE_SRC"/ext -type f`; do
-    SAGE_EXTCODE+="    \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"$'\n'
-done
-
-AC_SUBST([SAGE_EXTCODE])
-
 SAGE_MAKE_DEPS="$SAGE_ROOT/build/make/deps"
 AC_SUBST_FILE([SAGE_MAKE_DEPS])
 
 
 dnl AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([build/make/Makefile-auto build/make/Makefile src/Makefile])
-AC_CONFIG_FILES([src/bin/sage-env-config])
+AC_CONFIG_FILES([src/bin/sage-env-config build/bin/sage-build-env-config])
 
 AC_CONFIG_FILES([build/pkgs/sage_conf/src/sage_conf.py build/pkgs/sage_conf/src/setup.cfg])
 

src/bin/sage

@@ -137,6 +137,9 @@ usage_advanced() {
     echo "  -R [...]            -- run Sage's R with given arguments"
     echo "  -scons [...]        -- run Sage's scons"
     echo "  -sh [...]           -- run \$SHELL ($SHELL) with Sage environment variables"
+    echo "                         as they are set in the runtime of Sage"
+    echo "  -buildsh [...]      -- run \$SHELL ($SHELL) with Sage environment variables"
+    echo "                         as they are set while building Sage and its packages"
     echo "  -singular [...]     -- run Sage's singular with given arguments"
     echo "  -sqlite3 [...]      -- run Sage's sqlite3 with given arguments"
     echo "  -twistd [...]       -- run Twisted server"
@@ -660,13 +663,26 @@ if [ "$1" = '-git-branch' -o "$1" = '--git-branch' ]; then
     exec git --git-dir="$SAGE_ROOT"/.git rev-parse --abbrev-ref HEAD
 fi
 
-if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
+if [ "$1" = '-sh' -o "$1" = '--sh' -o "$1" = '-buildsh' -o "$1" = '--buildsh' ]; then
     # AUTHORS:
     # - Carl Witty and William Stein: initial version
     # - Craig Citro: add options for not loading profile
     # - Martin Albrecht: fix zshell prompt (#11866)
     # - John Palmieri: shorten the prompts, and don't print messages if
     #   there are more arguments to 'sage -sh' (#11790)
+    if [ -z "$SAGE_SHPROMPT_PREFIX" ]; then
+        SAGE_SHPROMPT_PREFIX=sage-sh
+    fi
+    if [ "$1" = '-buildsh' -o "$1" = '--buildsh' ]; then
+        if [ ! -r "$SAGE_ROOT"/build/bin/sage-build-env-config ]; then
+           echo "error: '$SAGE_ROOT' does not contain build/bin/sage-build-env-config.  Run configure first."
+           exit 1
+        fi
+        . "$SAGE_ROOT"/build/bin/sage-build-env-config || (echo "error:  Error sourcing $SAGE_ROOT/build/bin/sage-build-env-config"; exit 1)
+        export SAGE_SHPROMPT_PREFIX=sage-buildsh
+        # We export it so that recursive invocation of 'sage-sh' from a sage-buildsh shows the sage-buildsh prompt;
+        # this makes sense because all environment variables set in build/bin/sage-build-env-config are exported.
+    fi
     shift
     # If $SHELL is unset, default to bash
     if [ -z "$SHELL" ]; then
@@ -693,9 +709,9 @@ if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
         bash)
             SHELL_OPTS="--norc"
             if [ "$color_prompt" = yes ]; then
-                PS1="\[$(tput rev)\](sage-sh)\[$(tput sgr0)\] \u@\h:\W\$ "
+                PS1="\[$(tput rev)\]($SAGE_SHPROMPT_PREFIX)\[$(tput sgr0)\] \u@\h:\W\$ "
             else
-                PS1="(sage-sh) \u@\h:\w\$ "
+                PS1="($SAGE_SHPROMPT_PREFIX) \u@\h:\w\$ "
             fi
             export PS1
             ;;
@@ -708,9 +724,9 @@ if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
         ksh)
             SHELL_OPTS="-p"
             if [ "$color_prompt" = yes ] ; then
-                PS1="$(tput rev)(sage-sh)$(tput sgr0) $USER@`hostname -s`:\${PWD##*/}$ "
+                PS1="$(tput rev)($SAGE_SHPROMPT_PREFIX)$(tput sgr0) $USER@`hostname -s`:\${PWD##*/}$ "
             else
-                PS1="(sage-sh) $USER@`hostname -s`:\${PWD##*/}$ "
+                PS1="($SAGE_SHPROMPT_PREFIX) $USER@`hostname -s`:\${PWD##*/}$ "
             fi
             export PS1
             ;;
@@ -719,9 +735,9 @@ if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
             # bash, but this is not guaranteed), so we don't set
             # SHELL_OPTS.
             if [ "$color_prompt" = yes ] ; then
-                PS1="$(tput rev)(sage-sh)$(tput sgr0) $USER@`hostname -s`:\${PWD##*/}$ "
+                PS1="$(tput rev)($SAGE_SHPROMPT_PREFIX)$(tput sgr0) $USER@`hostname -s`:\${PWD##*/}$ "
             else
-                PS1="(sage-sh) $USER@`hostname -s`:\${PWD}$ "
+                PS1="($SAGE_SHPROMPT_PREFIX) $USER@`hostname -s`:\${PWD}$ "
             fi
             export PS1
             ;;
@@ -732,7 +748,7 @@ if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
             SHELL_OPTS="-f"
             ;;
         zsh)
-            PS1="%S(sage-sh)%s %n@%m:%~$ "
+            PS1="%S($SAGE_SHPROMPT_PREFIX)%s %n@%m:%~$ "
             # In zsh, the system /etc/zshenv is *always* run,
             # and this may change the path (like on OSX), so we'll
             # create a temporary .zshenv to reset the path
@@ -744,7 +760,7 @@ EOF
             export PS1
             ;;
         *)
-            export PS1='(sage-sh) $ '
+            export PS1='($SAGE_SHPROMPT_PREFIX) $ '
             ;;
     esac
     if [ -n "$oldPS1" ]; then

src/bin/sage-env

@@ -283,7 +283,6 @@ fi
 # depending on SAGE_ROOT and SAGE_LOCAL which are already defined.
 export SAGE_ETC="$SAGE_LOCAL/etc"
 export SAGE_SHARE="$SAGE_LOCAL/share"
-export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
 export SAGE_PKGCONFIG="$SAGE_LOCAL/lib/pkgconfig"
 export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
 export SAGE_SPKG_SCRIPTS="$SAGE_LOCAL/var/lib/sage/scripts"