Merge tag '9.3.beta8' into t/31335/homebrew__unused_packages__singula…

…r__pari_______in__usr_local_leak_into_sagelib_build

SageMath version 9.3.beta8, Release Date: 2021-03-07

.github/workflows/extract-sage-local.sh

@@ -1,26 +1,27 @@
 #!/usr/bin/env bash
 # to be run from $SAGE_ROOT, with arguments sage-local-${{ env.PREVIOUS_STAGES }}.tar
 
+if [ -z "$SAGE_LOCAL" ]; then
+    SAGE_LOCAL=$(pwd)/local
+fi
+
 # Show all tar files
 ls -l $*
 
 # We specifically use the cygwin tar so that symlinks are saved/restored correctly on Windows.
 for a in $*; do
     echo Extracting $a
-    tar xf $a
+    (cd / && tar xf -) < $a
     rm -f $a
 done
 
-# Also get rid of the stages that were not extracted
-rm -f sage-local-*.tar
-
 # We set the installation records to the same mtime so that no rebuilds due to dependencies
 # among these packages are triggered.
-(cd local/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
+(cd "$SAGE_LOCAL"/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
 
 # Show what has been built already.
-ls -l local local/var/lib/sage/installed/
+ls -l "$SAGE_LOCAL" "$SAGE_LOCAL"/var/lib/sage/installed/
 df -h
 
 # Rebase!
-src/bin/sage-rebase.sh local
+src/bin/sage-rebase.sh "$SAGE_LOCAL"

.github/workflows/tox-experimental.yml

@@ -62,7 +62,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - 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

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - 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: |
@@ -114,7 +114,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.

.github/workflows/tox-optional.yml

@@ -64,7 +64,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - 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

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - 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: |
@@ -163,7 +163,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.

.gitignore

@@ -101,7 +101,7 @@ src/sage/modular/arithgroup/farey_symbol.h
 !src/sage/cpython/debugimpl.c
 !src/sage/graphs/base/boost_interface.cpp
 !src/sage/graphs/cliquer/cl.c
-!src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp
+!src/sage/graphs/graph_decompositions/sage_tdlib.cpp
 !src/sage/libs/eclib/wrap.cpp
 !src/sage/misc/inherit_comparison_impl.c
 !src/sage/modular/arithgroup/farey.cpp

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta7", 
-    "version": "9.3.beta7", 
+    "title": "sagemath/sage: 9.3.beta8", 
+    "version": "9.3.beta8", 
     "upload_type": "software", 
-    "publication_date": "2021-02-07", 
+    "publication_date": "2021-03-07", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta7", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta8", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.beta7, Release Date: 2021-02-07
+SageMath version 9.3.beta8, Release Date: 2021-03-07

build/bin/sage-build-env

@@ -24,34 +24,34 @@
 # The compiler flags are set in order of priority by
 # 1) environment variables
 # 2) flags set at configuration time
-if [ "x$CFLAGS" == "x" ]; then
+if [ "x$CFLAGS" = "x" ]; then
     export ORIGINAL_CFLAGS="$CONFIGURED_CFLAGS"
 else
     export ORIGINAL_CFLAGS="$CFLAGS"
 fi
-if [ "x$CXXFLAGS" == "x" ]; then
+if [ "x$CXXFLAGS" = "x" ]; then
     export ORIGINAL_CXXFLAGS="$CONFIGURED_CXXFLAGS"
 else
     export ORIGINAL_CXXFLAGS="$CXXFLAGS"
 fi
-if [ "x$FCFLAGS" == "x" ]; then
+if [ "x$FCFLAGS" = "x" ]; then
     export ORIGINAL_FCFLAGS="$CONFIGURED_FCFLAGS"
 else
     export ORIGINAL_FCFLAGS="$FCFLAGS"
 fi
-if [ "x$F77FLAGS" == "x" ]; then
+if [ "x$F77FLAGS" = "x" ]; then
     export ORIGINAL_F77FLAGS="$CONFIGURED_F77FLAGS"
 else
     export ORIGINAL_F77FLAGS="$F77FLAGS"
 fi
 
 # We optimize according to $SAGE_DEBUG.
-if [ "x$ORIGINAL_CFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_CFLAGS" = "x" ]; then
     # Evaluate SAGE_DEBUG:
-    if [ "x$SAGE_DEBUG" == "xyes" ]; then
+    if [ "x$SAGE_DEBUG" = "xyes" ]; then
         export CFLAGS_NON_NATIVE="-Og -g"
         export CFLAGS_O3_NON_NATIVE="-Og -g"
-    elif [ "x$SAGE_DEBUG" == "xno" ]; then
+    elif [ "x$SAGE_DEBUG" = "xno" ]; then
         export CFLAGS_NON_NATIVE="-O2"
         export CFLAGS_O3_NON_NATIVE="-O3"
     else
@@ -69,7 +69,7 @@ else
 fi
 
 # Copy to CXXFLAGS if this is not set.
-if [ "x$ORIGINAL_CXXFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_CXXFLAGS" = "x" ]; then
     export CXXFLAGS="$CFLAGS"
     export CXXFLAGS_O3="$CFLAGS_O3"
     export CXXFLAGS_NON_NATIVE="$CFLAGS_NON_NATIVE"
@@ -82,7 +82,7 @@ else
 fi
 
 # Copy CFLAGS to FCFLAGS if this is not set.
-if [ "x$ORIGINAL_FCFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_FCFLAGS" = "x" ]; then
     export FCFLAGS="$CFLAGS"
     export FCFLAGS_O3="$CFLAGS_O3"
     export FCFLAGS_NON_NATIVE="$CFLAGS_NON_NATIVE"
@@ -95,7 +95,7 @@ else
 fi
 
 # Copy FCFLAGS to F77FLAGS if this is not set.
-if [ "x$ORIGINAL_F77FLAGS" == "x" ]; then
+if [ "x$ORIGINAL_F77FLAGS" = "x" ]; then
     export F77FLAGS="$FCFLAGS"
     export F77FLAGS_O3="$FCFLAGS_O3"
     export F77FLAGS_NON_NATIVE="$FCFLAGS_NON_NATIVE"

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

@@ -27,7 +27,7 @@ export SAGE_FAT_BINARY="@SAGE_FAT_BINARY@"
 
 # Export SAGE_DEBUG if this was enabled during configure,
 # but be respectful of the current settings.
-if [ "x$SAGE_DEBUG" == "x" ]; then
+if [ "x$SAGE_DEBUG" = "x" ]; then
     export SAGE_DEBUG="@SAGE_DEBUG@"
 fi
 

build/bin/sage-dist-helpers

@@ -227,17 +227,14 @@ sdh_pip_install() {
     sdh_store_and_pip_install_wheel .
 }
 
-sdh_store_and_pip_install_wheel() {
+sdh_store_wheel() {
     if [ -n "$SAGE_DESTDIR" ]; then
         local sudo=""
-        # --no-warn-script-location: Suppress a warning caused by --root
-        local root="--root=$SAGE_DESTDIR --no-warn-script-location"
     else
         local sudo="$SAGE_SUDO"
-        local root=""
     fi
     if [ "$*" != "." ]; then
-        sdh_die "Error: sdh_store_and_pip_install_wheel requires . as only argument"
+        sdh_die "Error: sdh_store_wheel requires . as only argument"
     fi
     wheel=""
     for w in dist/*.whl; do
@@ -252,11 +249,24 @@ sdh_store_and_pip_install_wheel() {
         sdh_die "Error: no wheel found after building"
     fi
 
-    $sudo sage-pip-install $root "$wheel" || \
-        sdh_die "Error installing $wheel"
     mkdir -p "${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}" && \
         $sudo mv "$wheel" "${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}/" || \
         sdh_die "Error storing $wheel"
+    wheel="${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}/${wheel##*/}"
+}
+
+sdh_store_and_pip_install_wheel() {
+    sdh_store_wheel "$@"
+    if [ -n "$SAGE_DESTDIR" ]; then
+        local sudo=""
+        # --no-warn-script-location: Suppress a warning caused by --root
+        local root="--root=$SAGE_DESTDIR --no-warn-script-location"
+    else
+        local sudo="$SAGE_SUDO"
+        local root=""
+    fi
+    $sudo sage-pip-install $root "$wheel" || \
+        sdh_die "Error installing ${wheel##*/}"
 }
 
 sdh_cmake() {

build/bin/sage-print-system-package-command

@@ -5,7 +5,11 @@ shift
 IF_VERBOSE=:
 SUDO=
 PROMPT=
-COMMENT="# "
+if [ -n "$OUTPUT_RST" ]; then
+    COMMENT=""
+else
+    COMMENT="# "
+fi
 while :
 do
     case "$1" in
@@ -51,6 +55,25 @@ system_packages="$*"
 options=
 env=
 shopt -s extglob
+
+function print_shell_command()
+{
+    if [ -n "$OUTPUT_RST" ]; then
+        echo
+        echo ".. CODE-BLOCK:: bash"
+        echo
+    fi
+    echo "${PROMPT}$1"
+    if [ -n "$OUTPUT_RST" ]; then
+        echo
+    fi
+}
+
+function print_comment()
+{
+    echo "${COMMENT}$1"
+}
+
 case $system:$command in
     homebrew*:setup-build-env)
         $IF_VERBOSE echo "${COMMENT}"
@@ -70,66 +93,79 @@ case $system:$command in
     # Verbs handled above are our own inventions. Verbs handled below are apt-get verbs.
     #
     @(debian*|ubuntu*):update)
-        echo "${PROMPT}${SUDO}apt-get $command $system_packages"
+        print_shell_command "${SUDO}apt-get $command $system_packages"
         ;;
     @(debian*|ubuntu*):*)
         [ "$NO_INSTALL_RECOMMENDS" = yes ] && options="$options --no-install-recommends"
         [ "$YES" = yes ] && options="$options --yes" env="DEBIAN_FRONTEND=noninteractive "
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}${env}apt-get $command $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}${env}apt-get $command $options $system_packages"
         ;;
     @(fedora*|redhat*|centos*):install)
         [ "$YES" = yes ] && options="$options -y"
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}yum install $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}yum install $options $system_packages"
         ;;
     gentoo*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}emerge $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}emerge $system_packages"
         ;;
     arch*:update)
-        echo "${PROMPT}${SUDO}pacman -Sy"
+        print_shell_command "${SUDO}pacman -Sy"
         ;;
     arch*:install)
         [ "$YES" = yes ] && options="$options --noconfirm"
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}pacman -S $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}pacman -S $options $system_packages"
         ;;
     void*:update)
-        echo "${PROMPT}${SUDO}xbps-install -Su"
+        print_shell_command "${SUDO}xbps-install -Su"
         ;;
     void*:install)
         [ "$YES" = yes ] && options="$options --yes"
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}xbps-install $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}xbps-install $options $system_packages"
         ;;
     opensuse*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}zypper install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}zypper install $system_packages"
         ;;
     *conda*:install)
         [ "$YES" = yes ] && options="$options --yes"
-        [ -n "$system_packages" ] && echo "${PROMPT}conda install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "conda install $system_packages"
         ;;
     homebrew*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}brew install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "brew install $system_packages"
         ;;
     slackware*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}slackpkg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}slackpkg install $system_packages"
         ;;
     cygwin*:update)
-        echo "# first install apt-cyg from https://github.com/transcode-open/apt-cyg"
+        print_commment "first install apt-cyg from https://github.com/transcode-open/apt-cyg"
         ;;
     cygwin*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}apt-cyg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "apt-cyg install $system_packages"
         ;;
     freebsd*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}pkg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "${SUDO}pkg install $system_packages"
         ;;
     nix*:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}nix-env --install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "nix-env --install $system_packages"
         ;;
     pip:install)
-        [ -n "$system_packages" ] && echo "${PROMPT}sage -pip install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command "sage -pip install $system_packages"
+        ;;
+    repology:install)
+        if [ -n "$system_packages" ]; then
+            links=""
+            for pkg in $system_packages; do
+                link="https://repology.org/project/$pkg/versions"
+                if [ -n "$links" ]; then
+                    links="$links, "
+                fi
+                links="$links$link"
+            done
+            print_comment "See ${links}"
+        fi
         ;;
     *:update)
         # Nothing needed
         ;;
     *)
-        echo "# $command the following packages: $system_packages"
+        print_comment "$command the following packages: $system_packages"
         ;;
 esac