Merge tag '9.3.rc2' into t/31554/public/31554

SageMath version 9.3.rc2, Release Date: 2021-04-06

.github/workflows/tox-experimental.yml

@@ -54,15 +54,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox-gcc_spkg.yml

@@ -52,15 +52,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox-optional.yml

@@ -56,15 +56,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox.yml

@@ -52,15 +52,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.rc1", 
-    "version": "9.3.rc1", 
+    "title": "sagemath/sage: 9.3.rc2", 
+    "version": "9.3.rc2", 
     "upload_type": "software", 
-    "publication_date": "2021-03-29", 
+    "publication_date": "2021-04-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc2", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.rc1, Release Date: 2021-03-29
+SageMath version 9.3.rc2, Release Date: 2021-04-06

build/pkgs/cddlib/checksums.ini

@@ -1,5 +1,5 @@
 tarball=cddlib-VERSION.tar.gz
-sha1=4bad24b32d9c056615377ff3103e6b95e17628ac
-md5=73e5f7dfa72b5c3339c09564721813d6
-cksum=3211115816
+sha1=8f38597a0479a191a62346dab89794e888c478b6
+md5=ec7f35912e34232b5306a643f99b6311
+cksum=2420656558
 upstream_url=https://github.com/cddlib/cddlib/releases/download/VERSION/cddlib-VERSION.tar.gz

build/pkgs/cddlib/package-version.txt

@@ -1 +1 @@
-0.94j
+0.94m

build/pkgs/cddlib/spkg-configure.m4

@@ -16,14 +16,39 @@ SAGE_SPKG_CONFIGURE([cddlib], [
     AC_CHECK_PROGS(SCDD, [scdd_gmp scdd])
     AS_IF([test x$SCDD = x], [sage_spkg_install_cddlib=yes])
 
-    dnl Future versions (>= 0.94k) of cddlib will put these headers in
+    dnl https://trac.sagemath.org/ticket/30319
+    AS_IF([test -n "$CDDEXEC"], [
+        AC_MSG_CHECKING([whether $CDDEXEC --redcheck works correctly for real input])
+        cat > conftest.ine <<EOF
+H-representation
+linearity 2 1 2
+begin
+ 5 4 real
+ 0.0 0.0 1.0 1.0
+ -1.0 0.0 1.0 1.0
+ -1.0 2.0 -1.0 0.0
+ -1.0 4.0 -2.0 0.0
+ 1 0 0 0
+end
+EOF
+        rm -f conftest.out
+        $CDDEXEC --redcheck <conftest.ine >conftest.out 2>& AS_MESSAGE_LOG_FD
+        AS_IF([grep -q "^Redundant rows.*1" conftest.out 2>& AS_MESSAGE_LOG_FD], [
+            AC_MSG_RESULT([no])
+            sage_spkg_install_cddlib=yes
+        ], [
+            AC_MSG_RESULT([yes])
+        ])
+    ])
+    dnl Recent versions (>= 0.94k) of cddlib put these headers in
     dnl a "cddlib" subdirectory, and Debian currently relocates them
     dnl under "cdd". But for now they're at the top-level, in e.g.
     dnl /usr/include/cdd.h. The lattE and gfan packages within
     dnl SageMath both look for them there, so that's where we have to
     dnl check, passing up a chance to detect cddlib on Fedora and Debian
     dnl for now. Once all of cddlib's consumers know about the new (or
     dnl both) locations, we can update this check to support them.
+    dnl See https://trac.sagemath.org/ticket/29413
     AC_CHECK_HEADER([cdd.h],[],[sage_spkg_install_cddlib=yes],[
       #include <setoper.h>
       #include <cddmp.h>

build/pkgs/cddlib/spkg-install.in

@@ -5,3 +5,10 @@ cd src
 sdh_configure
 sdh_make
 sdh_make_install
+
+# Old versions of cddlib install headers without the official prefix "cddlib/";
+# and some distributions install the headers with a prefix "cdd/".
+# We install symlinks to shadow possible system installations of these headers.
+# This can be removed as soon as all packages that detect cddlib have been
+# updated to check the official prefix "cddlib/" first.
+(cd $SAGE_DESTDIR$SAGE_LOCAL/include/ && ln -sf cddlib cdd && ln -sf cddlib/*.h .)

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=df2f6839c4a19b7d21c4f387df24596fcfa2b459
-md5=f307be6d68e25b3924cc93d2bcc9dc04
-cksum=1158861891
+sha1=08f282239756f779e6b97cf391fbd0e22d6129a9
+md5=49062bca12e661eaa98631ae44e843bf
+cksum=1707016786

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-6e084f9dbad96c3a166732efb36fe71acd2e7ba2
+4275b275a2cb292826cdeb078765331dcda54c96

build/pkgs/cvxopt/spkg-install.in

@@ -65,9 +65,9 @@ export CVXOPT_BLAS_LIB="$(cvxopt_output l blas)"
 export CVXOPT_BLAS_LIB_DIR="$(pkg-config --variable=libdir blas)"
 export CVXOPT_LAPACK_LIB="$(cvxopt_output l lapack)"
 
-if test "x$SAGE_SUITESPARSE_LOCALINSTALL" != "x"; then
-   export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_LOCAL}"
-   export CVXOPT_SUITESPARSE_INC_DIR="${SAGE_LOCAL}/include"
+if test "x$SAGE_SUITESPARSE_PREFIX" != "x"; then
+   export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_SUITESPARSE_PREFIX}"
+   export CVXOPT_SUITESPARSE_INC_DIR="${SAGE_SUITESPARSE_PREFIX}/include"
 fi
 
 export CVXOPT_BUILD_GLPK=1

build/pkgs/ipywidgets/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) widgetsnbextension | $(PYTHON_TOOLCHAIN)
+$(PYTHON) widgetsnbextension | $(PYTHON_TOOLCHAIN) ipykernel ipython traitlets
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/openssl/spkg-install.in

@@ -1,9 +1,4 @@
-if [ -z "$SAGE_LOCAL" ]; then
-    echo >&2 "SAGE_LOCAL undefined ... exiting"
-    echo >&2 "Maybe run 'sage --sh'?"
-    exit 1
-fi
-
+# -*- shell-script -*-
 cd src
 
 # ./config picks up these environment variables if they are set, instead of using uname components
@@ -12,26 +7,24 @@ unset RELEASE
 unset SYSTEM
 unset BUILD
 
-# Building on OS X Lion 64-bit seems to fail unless we build a 64-bit library.
+extra_config_args=
+target=$($CC -dumpmachine 2> /dev/null)
 echo
-echo "Configuring openssl..."
-./config --prefix="$SAGE_LOCAL" --openssldir="$SAGE_LOCAL"/openssl shared
+echo "Configuring openssl for target reported by $CC -dumpmachine: $target"
+case "$target" in
+    # Trac #31538: On 64 bit kernels running a 32 bit system, use the target of
+    # the configured compiler
+    i?86-*linux*)
+        extra_config_args="linux-x86"
+        ;;
+esac
 
-echo "Building openssl..."
-$MAKE
-
-if [ $? -ne 0 ]; then
-    echo >&2 "Error building openssl."
-    exit 1
-fi
-echo
+./config --prefix="$SAGE_LOCAL" --openssldir="$SAGE_LOCAL"/openssl shared $extra_config_args
 
 
+echo "Building openssl..."
+$MAKE || sdh_die "Error building openssl."
 
 echo "Installing openssl..."
 # installing the docs fails often, skip
-$MAKE install_sw
-if [ $? -ne 0 ]; then
-    echo >&2 "Error installing openssl."
-    exit 1
-fi
+$MAKE install_sw || sdh_die "Error installing openssl."

build/pkgs/pynac/package-version.txt

@@ -1 +1 @@
-0.7.27.p2
+0.7.27.p3

build/pkgs/pynac/patches/too_much_sub.patch

@@ -0,0 +1,15 @@
+diff --git a/ginac/power.cpp b/ginac/power.cpp
+index 5c07324..837fce3 100644
+--- a/ginac/power.cpp
++++ b/ginac/power.cpp
+@@ -745,6 +745,10 @@ ex power::subs(const exmap & m, unsigned options) const
+         if (!are_ex_trivially_equal(basis, subsed_basis)
+ 	 || !are_ex_trivially_equal(exponent, subsed_exponent)) {
+ 		ex p = power(subsed_basis, subsed_exponent);
++		if (!is_exactly_a<power>(p)) {
++		    // trac 30378 and 31530: do not over-substitute
++	        return p;
++	    }
+                 ex t = ex_to<power>(p).subs_one_level(m, options);
+                 if ((t-*this).is_zero())
+                         return p;

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.3.rc1
+9.3.rc2

build/pkgs/singular/checksums.ini

@@ -1,5 +1,5 @@
 tarball=singular-VERSION.tar.gz
-sha1=eeb0b250e481e710daea45c2f78ccff9b84e6f15
-md5=88c4500c2d6ac3eb9b112111fc9404ad
-cksum=3131197750
-upstream_url=https://trac.sagemath.org/raw-attachment/ticket/25993/singular-VERSION.tar.gz
+sha1=3c8e4d867a050d676f1eaee622694d30c1e00bcc
+md5=edd42d42f3ddaa4f495a2111c72bf0da
+cksum=1198605855
+upstream_url=https://trac.sagemath.org/raw-attachment/ticket/31552/singular-VERSION.tar.gz

build/pkgs/singular/package-version.txt

@@ -1 +1 @@
-4.2.0p1+2021-03-13+sage
+4.2.0p1+2021-03-24+sage-2

build/pkgs/suitesparse/spkg-configure.m4

@@ -17,8 +17,8 @@ SAGE_SPKG_CONFIGURE([suitesparse], [
       sage_spkg_install_suitesparse=yes])
 ], [], [], [
     AS_IF([test x$sage_spkg_install_suitesparse = xyes], [
-       AC_SUBST(SAGE_SUITESPARSE_LOCALINSTALL, ['$SAGE_LOCAL'])
+       AC_SUBST(SAGE_SUITESPARSE_PREFIX, ['$SAGE_LOCAL'])
     ], [
-       AC_SUBST(SAGE_SUITESPARSE_LOCALINSTALL, [''])
+       AC_SUBST(SAGE_SUITESPARSE_PREFIX, [''])
     ])
 ])

build/pkgs/tachyon/spkg-install.in

@@ -17,20 +17,20 @@ case "$UNAME" in
     TARGET=bsd
     ;;
 "Linux")
-    case "`uname -m`" in
-    i[3456]86)
+    case "$($CC -dumpmachine)" in
+    i[3456]86*)
         TARGET=linux-thr
         ;;
-    ia64)
+    ia64*)
         TARGET=linux-ia64-thr
         ;;
-    amd64|x86_64)
+    amd64*|x86_64*)
         TARGET=linux-64-thr
         ;;
     ppc*|powerpc*)
         TARGET=linux-ppc
         ;;
-    armv6l|armv7l)
+    armv6l*|armv7l*)
         TARGET=linux-arm-thr
         ;;
     esac

configure.ac

@@ -424,6 +424,14 @@ AC_ARG_ENABLE([notebook],
     done
   ])
 
+AC_ARG_ENABLE([r],
+  AS_HELP_STRING([--disable-r],
+                 [disable build of the R package and related packages]), [
+    for pkg in r rpy2 r_jupyter; do
+      AS_VAR_SET([SAGE_ENABLE_$pkg], [$enableval])
+    done
+  ])
+
 SAGE_SPKG_COLLECT()
 
 dnl AC_CONFIG_HEADERS([config.h])

src/VERSION.txt

@@ -1 +1 @@
-9.3.rc1
+9.3.rc2