Merge latest beta into docker-py3

.gitignore

@@ -38,6 +38,9 @@
 .idea
 .iml
 
+# VSCode
+.vscode
+
 # XCode
 xcuserdata/
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.8.rc1, Release Date: 2019-06-13
+SageMath version 8.9.beta7, Release Date: 2019-08-18

bootstrap

@@ -5,16 +5,18 @@
 #
 # If the -s option is given, save the autogenerated scripts in
 # $SAGE_ROOT/upstream/configure-$CONFVERSION.tar.gz where CONFVERSION
-# is the version number stored in
-# build/pkgs/configure/package-version.txt
-#
-# If optional argument -i is given, then automatically increment the
-# version number.
+# is the sha1 of HEAD `git rev-parse HEAD`
 #
 # If optional argument -d is given and bootstrapping failed, instead
 # extract the files from a local configure tarball, downloading it if
 # needed. If -D is given, don't try to bootstrap and always extract or
 # download.
+#
+# If optional argument -u <URL> is given download the configure
+# tarball from that base url. That is, "bootstrap -u http://host/path"
+# will download http://host/path/configure-$CONFVERSION.tar.gz to
+# upstream/configure-$CONFVERSION.tar.gz. This is used by the buildbot
+# to download tarballs that are not published.
 ########################################################################
 
 # Set SAGE_ROOT to the path to this file and then cd into it
@@ -25,7 +27,49 @@ export PATH="$SAGE_ROOT/build/bin:$PATH"
 
 PKG=build/pkgs/configure
 MAKE="${MAKE:-make}"
-CONFVERSION=`cat $PKG/package-version.txt`
+CONFVERSION=$(cat $PKG/package-version.txt)
+
+install_config_rpath() {
+    # The file config.rpath which comes from gettext is supposed to be
+    # installed by automake, but due to a bug in most distros it is not;
+    # see https://trac.sagemath.org/ticket/27823#comment:17
+    #
+    # Here we need to determine where gettext stores its data files and
+    # copy config.rpath from there to config/
+    gettextize="$(command -v gettextize)"
+    if [ -z "$gettextize" ]; then
+        echo >&2 "gettext and the gettextize program must be installed and be in"
+        echo >&2 "your PATH. E.g. Homebrew installs them in /usr/local/opt/gettext/bin."
+        return 179
+    fi
+    eval `sed -n '/^prefix=.*$/p' $gettextize`
+    eval `sed -n '/^datarootdir=.*$/p' $gettextize`
+    eval `sed -n '/^: \${gettext_datadir=.*$/p' $gettextize`
+
+    if [ -z "$gettext_datadir" ]; then
+        eval `sed -n '/^gettext_dir=.*$/p' $gettextize`
+        # In older versions (before 2014) this is spelled gettext_dir
+        # See https://github.com/autotools-mirror/gettext/commit/ff18897068486560e2bb421004cfbd42b7cdd0f8
+        gettext_datadir="$gettext_dir"
+    fi
+
+    if [ -z "$gettext_datadir" ]; then
+        echo >&2 "Failed to read the gettext_datadir directory from $gettextize"
+        echo >&2 "The config.rpath file must manually be copied into config/"
+        echo >&2 "This file is installed with gettext typically in /usr/share/gettext"
+        return 179
+    fi
+
+    config_rpath="$gettext_datadir/config.rpath"
+    if [ ! -f "$config_rpath" ]; then
+        echo >&2 "Missing $config_rpath file; this indicates a broken gettext install."
+        return 179
+    fi
+
+    echo "bootstrap:$LINENO: installing 'config/config.rpath'"
+    cp "$config_rpath" config/
+}
+
 
 
 bootstrap () {
@@ -39,6 +83,7 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
     done
     echo "$spkg_configures" >> m4/sage_spkg_configures.m4
 
+    install_config_rpath && \
     aclocal -I m4 && \
     automake --add-missing --copy build/make/Makefile-auto && \
     autoconf
@@ -47,7 +92,7 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
     case $st in
         0) true;; # Success
 
-        16|63|127)  # no m4 for pkg-config, or autotools not installed, or version too old
+        179|16|63|127)  # install_config_rpath failed|no m4 for pkg-config|autotools not installed|or version too old
             if [ $DOWNLOAD = yes ]; then
                 echo >&2 "Bootstrap failed, downloading required files instead."
                 bootstrap-download || exit $?
@@ -94,35 +139,39 @@ save () {
         exit 63
     fi
 
+    NEWCONFVERSION=`git rev-parse HEAD`
+    NEWCONFBALL="upstream/configure-$NEWCONFVERSION.tar.gz"
+
     # Create configure tarball
-    echo "Creating $CONFBALL..."
+    echo "Creating $NEWCONFBALL..."
     mkdir -p upstream
-    tar zcf "$CONFBALL" configure config/* build/make/Makefile-auto.in
+    tar zcf "$NEWCONFBALL" configure config/* build/make/Makefile-auto.in
 
-    # Update version number
-    echo "$CONFVERSION" >$PKG/package-version.txt
+    # Update version
+    echo "$NEWCONFVERSION" >$PKG/package-version.txt
 
     # Compute checksum
-    SAGE_ROOT=. src/bin/sage-fix-pkg-checksums "$CONFBALL"
+    ./sage --package fix-checksum configure
 }
 
 
 usage () {
-    echo >&2 "Usage: $0 [-d|-D|-s] [-i] [-h]"
+    echo >&2 "Usage: $0 [-d|-D|-s] [-u <URL>] [-h]"
 }
 
 
 # Parse options
 SAVE=no
 DOWNLOAD=no
 ALWAYSDOWNLOAD=no
-while getopts "Ddsih" OPTION
+CONFTARBALL_URL=""
+while getopts "Ddshu:" OPTION
 do
      case "$OPTION" in
          D) ALWAYSDOWNLOAD=yes; DOWNLOAD=yes;;
          d) DOWNLOAD=yes;;
          s) SAVE=yes;;
-         i) CONFVERSION=$(( CONFVERSION + 1 ));;
+         u) CONFTARBALL_URL="$OPTARG"; ALWAYSDOWNLOAD=yes; DOWNLOAD=yes;;
          h) usage; exit 0;;
          ?) usage; exit 2;;
      esac
@@ -146,7 +195,17 @@ source src/bin/sage-env 2>/dev/null
 
 
 if [ $ALWAYSDOWNLOAD = yes ]; then
-    bootstrap-download || exit $?
+    if [ -n "$CONFTARBALL_URL" ]; then
+        URL="$CONFTARBALL_URL"/configure-$CONFVERSION.tar.gz
+        sage-download-file "$URL" upstream/configure-$CONFVERSION.tar.gz
+        if [ $? -ne 0 ]; then
+            echo >&2 "Error: downloading configure-$CONFVERSION.tar.gz from $CONFTARBALL_URL failed"
+            exit 1
+        fi
+        echo >&2 "Downloaded configure-$CONFVERSION.tar.gz from $CONFTARBALL_URL "
+    else
+        bootstrap-download || exit $?
+    fi
 else
     bootstrap
 fi

build/bin/sage-spkg

@@ -678,14 +678,14 @@ write_script_wrapper() {
 export SAGE_ROOT="$SAGE_ROOT"
 export SAGE_SRC="$SAGE_SRC"
 export SAGE_PKG_DIR="$script_dir"
+export SAGE_SPKG_SCRIPTS="$SAGE_SPKG_SCRIPTS"
 
 export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"
 export PKG_VER="$PKG_VER"
 
-for lib in env dist-helpers; do
-    lib="sage-\$lib"
-    source "\$SAGE_SRC/bin/\$lib"
+for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env" ; do
+    source "\$lib"
     if [ \$? -ne 0 ]; then
         echo >&2 "Error: failed to source \$lib"
         echo >&2 "Is \$SAGE_ROOT the correct SAGE_ROOT?"

build/make/deps

@@ -124,6 +124,7 @@ base: $(inst_patch) $(inst_pkgconf)
 # dependencies for Cython files (e.g. PARI, NTL, MP_LIBRARY).
 sagelib: \
 		$(inst_arb) \
+		$(inst_boost_cropped) \
 		$(inst_$(BLAS)) \
 		$(inst_brial) \
 		$(inst_cliquer) \

build/pkgs/arb/spkg-configure.m4

@@ -0,0 +1,23 @@
+SAGE_SPKG_CONFIGURE([arb], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_FLINT])
+    SAGE_ARB_LIBRARY="arb"
+    AC_MSG_CHECKING([installing flint? ])
+    if test x$sage_spkg_install_flint = xyes; then
+        AC_MSG_RESULT([yes; install arb as well])
+        sage_spkg_install_arb=yes
+    else
+        AC_CHECK_HEADER(arb.h, [
+        dnl below function added in version 2.16 of arb
+            AC_CHECK_LIB([arb], [acb_mat_eig_simple], [],
+	      [dnl in Debian the name of dylib is different.
+               AC_CHECK_LIB([flint-arb], [acb_mat_eig_simple],
+                [SAGE_ARB_LIBRARY="flint-arb"], [sage_spkg_install_arb=yes])])
+        ], [sage_spkg_install_arb=yes])
+    fi
+], [], [], [
+    if test x$sage_spkg_install_arb = xyes; then
+        AC_SUBST(SAGE_ARB_LIBRARY,["arb"])
+    else
+        AC_SUBST(SAGE_ARB_LIBRARY,[$SAGE_ARB_LIBRARY])
+    fi
+])

build/pkgs/arb/spkg-install

@@ -4,8 +4,8 @@ cd src
 # be removed in arb >= 2.8 when it is released
 export EXTRA_SHARED_FLAGS=$LDFLAGS
 
-./configure --disable-static --prefix="$SAGE_LOCAL" --with-flint="$SAGE_LOCAL" \
-    $SAGE_CONFIGURE_GMP $SAGE_CONFIGURE_MPFR || \
+./configure --disable-static --prefix="$SAGE_LOCAL" $SAGE_CONFIGURE_GMP \
+            $SAGE_CONFIGURE_MPFR $SAGE_CONFIGURE_FLINT || \
     sdh_die "Error configuring arb."
 
 sdh_make verbose

build/pkgs/awali/SPKG.txt

@@ -0,0 +1,33 @@
+= awali =
+
+== Description ==
+
+Awali is a software platform dedicated to the computation of, and with, finite
+state machines. Here finite state machines is to be understood in the broadest
+possible sense: finite automata with output — often called transducers then — or
+even more generally finite automata with multiplicity, that is, automata that
+not only accept, or recognize, sequences of symbols but compute for every such
+sequence a `value' that is associated with it and which can be taken in any
+semiring. Hence the variety of situations that can thus be modellized.
+
+== License ==
+
+ * GPL 3.0
+
+== Upstream Contact ==
+
+ * Website: http://vaucanson-project.org/Awali/index.html
+ * Releases: http://files.vaucanson-project.org/tarballs/
+
+== Dependencies ==
+
+ * Python
+ * CMake
+ * Cython
+ * ncurses
+
+ * graphviz must be installed from your distro, and available in the path.
+
+== Special Update/Build Instructions ==
+
+  * None

build/pkgs/awali/checksums.ini

@@ -0,0 +1,4 @@
+tarball=awali-all-vVERSION.tgz
+sha1=9098aaefde031df58374bab0c1fc38109eecd4e3
+md5=d4216d8cbe21f83ae3a816a2f994f85e
+cksum=3149228485

build/pkgs/awali/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) cmake cython nbconvert ncurses
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/awali/package-version.txt

@@ -0,0 +1 @@
+1.0.2-190218

build/pkgs/awali/spkg-check

@@ -0,0 +1,2 @@
+cd src/_build
+sdh_make check

build/pkgs/awali/spkg-install

@@ -0,0 +1,12 @@
+cd src/
+
+mkdir _build
+cd _build
+cmake ..  -DINSTALL_DIR="${SAGE_LOCAL}" \
+          -DPYTHON=sage-python23 \
+          -DCORA=False
+
+sdh_make
+sdh_make b
+sdh_make install
+

build/pkgs/awali/type

@@ -0,0 +1 @@
+optional

build/pkgs/bleach/checksums.ini

@@ -1,4 +1,4 @@
 tarball=bleach-VERSION.tar.gz
-sha1=e7ee75050ccace055d5040010e3fdfb8e2535a3a
-md5=f042c4e8a953824dc8511f535daa20a4
-cksum=3095652578
+sha1=b44b7705a1425338cf429d66f009aa15d09b768d
+md5=fc8df989e0200a45f7a3a95ef9ee9854
+cksum=2528269335

build/pkgs/bleach/package-version.txt

@@ -1 +1 @@
-3.0.2
+3.1.0

build/pkgs/certifi/checksums.ini

@@ -1,4 +1,4 @@
 tarball=certifi-VERSION.tar.gz
-sha1=673bf8bc29d7ee0a1a0d8af74d050e5769fec2a9
-md5=8160cf662212bc731eccf1af8042c0af
-cksum=322391593
+sha1=f3873edcfc60c52e97e6601b2576ccdac419281a
+md5=76381d19d0a1171fecb2d1002b81424e
+cksum=2417220143

build/pkgs/certifi/package-version.txt

@@ -1 +1 @@
-2018.11.29
+2019.3.9

build/pkgs/configparser/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configparser-VERSION.tar.gz
-sha1=8ee6b29c6a11977c0e094da1d4f5f71e7e7ac78b
-md5=cfdd915a5b7a6c09917a64a573140538
-cksum=3139292895
+sha1=81351574c345e2a8600b7f2b2afb2b8f1c6aded2
+md5=aaa80b58b6b0810e54f66486860b3ed1
+cksum=4208301028

build/pkgs/configparser/package-version.txt

@@ -1 +1 @@
-3.5.0
+3.7.4

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=9655d2f1711ae231ce14a8ce519d9a2af0fb1dc4
-md5=28acd9297494c8171c44584c18efbd20
-cksum=1129046285
+sha1=e1f5fb67f8895c261043e4203c654772c15011e9
+md5=cb0bcc975697113d75adad861af22570
+cksum=593852789

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-324
+8c985712aebdb887c2e66308af1d29907a6fc242

build/pkgs/cryptominisat/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cryptominisat-VERSION.tar.gz
-sha1=568cd2f528609a31d217e24e381de87e011499d4
-md5=cce64bfd256700e96baee90b7bdfe770
-cksum=3567560229
+sha1=db418f5ac124e8d4e1f5284f05bccbe5b61afed9
+md5=ca1bf853e568c19968daa5464ab86843
+cksum=4204324235

build/pkgs/cryptominisat/package-version.txt

@@ -1 +1 @@
-5.6.6
+5.6.8

build/pkgs/curl/spkg-configure.m4

@@ -1,15 +1,26 @@
 SAGE_SPKG_CONFIGURE([curl], [
     # Only install curl (and libcurl) if we cannot find version 7.22 or
     # later, since that is what R needs.
-	AC_CACHE_CHECK([for curl 7.22], [ac_cv_path_CURL], [
-		AC_PATH_PROGS_FEATURE_CHECK([CURL], [curl], [
-		  ${ac_path_CURL}-config --checkfor 7.22 >/dev/null 2>/dev/null && ac_cv_path_CURL=${ac_path_CURL}
+    AC_CACHE_CHECK([for curl 7.22], [ac_cv_path_CURL], [
+        AC_PATH_PROGS_FEATURE_CHECK([CURL], [curl], [
+          ${ac_path_CURL}-config --checkfor 7.22 >/dev/null 2>/dev/null && ac_cv_path_CURL=${ac_path_CURL}
         ])
     ])
     AS_IF([test -z "$ac_cv_path_CURL"], [sage_spkg_install_curl=yes])
-    # If (lib)curl is installed, we need to check for the curl header
-    # file, too.
-    AS_IF([test $sage_spkg_install_curl = no], [
-        AC_CHECK_HEADER([curl/curl.h], [], [sage_spkg_install_curl=yes])
-    ])
+    LIBCURL_CHECK_CONFIG(, 7.22, , [sage_spkg_install_curl=yes])
+    # Anaconda on macOS provides a libcurl with @rpath. Check that
+    # linking produces a binary than can be run. (#27941)
+    AC_CACHE_CHECK([whether programs linking to libcurl can be executed],
+      [sage_libcurl_cv_lib_curl_executable],
+      [
+           _libcurl_save_cppflags=$CPPFLAGS
+           CPPFLAGS="$LIBCURL_CPPFLAGS $CPPFLAGS"
+           _libcurl_save_libs=$LIBS
+           LIBS="$LIBCURL $LIBS"
+
+           AC_RUN_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[
+             curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+           ]])], sage_libcurl_cv_lib_curl_executable=yes, sage_libcurl_cv_lib_curl_executable=no)
+      ])
+    AS_IF([test "$sage_libcurl_cv_lib_curl_executable" = "no"], [sage_spkg_install_curl=yes])
 ])

build/pkgs/cypari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cypari2-VERSION.tar.gz
-sha1=7f0a53f99079c110984ebe352c0848b87bfc2d62
-md5=84c05ca455bed3376a016d1073639ea2
-cksum=506281443
+sha1=d3fc80e83bafa3c7e6eb5a779de9395d4242dddc
+md5=9f431126112828c923f82e0393cbf317
+cksum=2176941985

build/pkgs/cypari/package-version.txt

@@ -1 +1 @@
-2.1.0.p0
+2.1.1