Merge branch 'develop' into test_imports

sagemath · Dec 28, 2023 · cc3792f · cc3792f
2 parents 97a2548 + e249bef
commit cc3792f
Show file tree

Hide file tree

Showing 739 changed files with 5,373 additions and 3,703 deletions.
diff --git a/.github/workflows/doc-build-pdf.yml b/.github/workflows/doc-build-pdf.yml
@@ -57,7 +57,7 @@ jobs:
           export PATH="build/bin:$PATH"
           eval $(sage-print-system-package-command auto update)
           eval $(sage-print-system-package-command auto --yes --no-install-recommends install zip)
-          eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git texlive)
+          eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git texlive texlive_luatex free_fonts xindy)
 
       - name: Add prebuilt tree as a worktree
         id: worktree

diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml
@@ -161,7 +161,7 @@ jobs:
           export PATH="build/bin:$PATH"
           eval $(sage-print-system-package-command auto update)
           eval $(sage-print-system-package-command auto --yes --no-install-recommends install zip)
-          eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git texlive)
+          eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git texlive texlive_luatex free_fonts xindy)
           export SAGE_USE_CDNS=yes
           export SAGE_LIVE_DOC=yes
           export SAGE_JUPYTER_SERVER=binder:sagemath/sage-binder-env/dev

diff --git a/CITATION.cff b/CITATION.cff
@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.3.beta3
+version: 10.3.beta4
 doi: 10.5281/zenodo.593563
-date-released: 2023-12-18
+date-released: 2023-12-26
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 10.3.beta3, Release Date: 2023-12-18
+SageMath version 10.3.beta4, Release Date: 2023-12-26
diff --git a/build/bin/sage-dist-helpers b/build/bin/sage-dist-helpers
@@ -244,7 +244,7 @@ sdh_pip_install() {
                 # Our default after #33789 (Sage 9.7): We allow the package to provision
                 # its build environment using the stored wheels.
                 # We pass --find-links.
-                # The SPKG needs to declare "setuptools_wheel" as a dependency.
+                # The SPKG needs to declare "setuptools" as a dependency.
                 build_isolation_option="--find-links=$SAGE_SPKG_WHEELS"
                 ;;
             --no-build-isolation)

diff --git a/build/bin/sage-get-system-packages b/build/bin/sage-get-system-packages
@@ -41,7 +41,7 @@ case "$SYSTEM" in
             fi
         fi
         SYSTEM_PACKAGES_FILE_NAMES="distros/$SYSTEM.txt"
-        STRIP_COMMENTS="sed s/#.*//;"
+        STRIP_COMMENTS="sed s/#.*//;s/\${PYTHON_MINOR}/${PYTHON_MINOR}/g"
         COLLECT=echo
         ;;
 esac

diff --git a/build/bin/sage-guess-package-system b/build/bin/sage-guess-package-system
@@ -11,6 +11,8 @@ if conda --version > /dev/null 2>&1; then
 fi
 if brew --version > /dev/null 2>&1; then
     echo homebrew
+elif port version > /dev/null 2>&1; then
+    echo macports
 elif emerge --version > /dev/null 2>&1; then
     echo gentoo
 elif apt-get --version > /dev/null 2>&1; then

diff --git a/build/bin/sage-print-system-package-command b/build/bin/sage-print-system-package-command
@@ -34,6 +34,16 @@ do
             ;;
         --prompt)
             PROMPT='  $ '
+            CONTINUATION='        '
+            ;;
+        --continuation=*)
+            CONTINUATION="${1#--continuation=}"
+            ;;
+        --wrap)
+            WRAP=78
+            ;;
+        --wrap=*)
+            WRAP="${1#--wrap=}"
             ;;
         --no-install-recommends)
             NO_INSTALL_RECOMMENDS=yes
@@ -79,7 +89,13 @@ function print_shell_command()
         echo ".. CODE-BLOCK:: bash"
         echo
     fi
-    echo "${PROMPT}$1"
+    # shell-quote arguments if necessary
+    quoted=$(for a in "$@"; do printf "%q " $a; done)
+    if [ -z "$WRAP" -o $# -lt 6 ]; then
+        echo "${PROMPT}${quoted}"
+    else
+        sage-bootstrap-python -c "import textwrap; print(' \\\\\n'.join(textwrap.wrap(r'''${quoted}''', $WRAP, initial_indent=r'''${PROMPT}''', subsequent_indent=r'''${CONTINUATION}''', break_long_words=False, break_on_hyphens=False)))"
+    fi
     if [ -n "$OUTPUT_RST" ]; then
         echo
     fi
@@ -102,77 +118,90 @@ case $system:$command in
         [ -n "$SAGE_ROOT" ] || SAGE_ROOT=.
         echo "${PROMPT}source $SAGE_ROOT/.homebrew-build-env"
         ;;
+    macports*:setup-build-env)
+        $IF_VERBOSE echo "${COMMENT}"
+        $IF_VERBOSE echo "${COMMENT}WARNING: Use of MacPorts is experimental"
+        $IF_VERBOSE echo "${COMMENT}"
+        $IF_VERBOSE echo "${COMMENT}MacPorts does not provide unversioned gfortran executables by default"
+        $IF_VERBOSE echo "${COMMENT}To make gfortran available (and build with gcc from XCode), use:"
+        $IF_VERBOSE echo "${COMMENT}"
+        $IF_VERBOSE print_shell_command ./configure FC=gfortran-mp-11
+        ;;
     *:setup-build-env)
         # Nothing needed
         ;;
     #
     # Verbs handled above are our own inventions. Verbs handled below are apt-get verbs.
     #
     @(debian*|ubuntu*):update)
-        print_shell_command "${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" ] && print_shell_command "${SUDO}${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" ] && print_shell_command "${SUDO}yum install $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}yum install $options $system_packages
         ;;
     gentoo*:install)
-        [ -n "$system_packages" ] && print_shell_command "${SUDO}emerge $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}emerge $system_packages
         ;;
     arch*:update)
         print_shell_command "${SUDO}pacman -Sy"
         ;;
     arch*:install)
         [ "$YES" = yes ] && options="$options --noconfirm"
-        [ -n "$system_packages" ] && print_shell_command "${SUDO}pacman -S $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}pacman -S $options $system_packages
         ;;
     void*:update)
         print_shell_command "${SUDO}xbps-install -Su"
         ;;
     void*:install)
         [ "$YES" = yes ] && options="$options --yes"
-        [ -n "$system_packages" ] && print_shell_command "${SUDO}xbps-install $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}xbps-install $options $system_packages
         ;;
     opensuse*:install)
-        [ -n "$system_packages" ] && print_shell_command "${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" ] && print_shell_command "conda install $options $system_packages"
+        [ -n "$system_packages" ] && print_shell_command conda install $options $system_packages
         ;;
     homebrew*:install)
-        [ -n "$system_packages" ] && print_shell_command "brew install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command brew install $system_packages
+        ;;
+    macports*:install)
+        [ "$YES" = yes ] && options="$options -N"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}port $options install $system_packages
         ;;
     slackware*:install)
-        [ -n "$system_packages" ] && print_shell_command "${SUDO}slackpkg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}slackpkg install $system_packages
         ;;
     cygwin*:update)
         print_comment "first install apt-cyg from https://github.com/transcode-open/apt-cyg"
         ;;
     cygwin*:install)
-        [ -n "$system_packages" ] && print_shell_command "apt-cyg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command apt-cyg install $system_packages
         ;;
     freebsd*:install)
-        [ -n "$system_packages" ] && print_shell_command "${SUDO}pkg install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command ${SUDO}pkg install $system_packages
         ;;
     nix*:install)
-        [ -n "$system_packages" ] && print_shell_command "nix-env --install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command nix-env --install $system_packages
         ;;
     alpine:update)
         print_shell_command "apk update"
         ;;
     alpine:install)
-        [ -n "$system_packages" ] && print_shell_command "apk add $system_packages"
+        [ -n "$system_packages" ] && print_shell_command apk add $system_packages
         ;;
     pip:install)
-        [ -n "$system_packages" ] && print_shell_command "sage -pip install $system_packages"
+        [ -n "$system_packages" ] && print_shell_command sage -pip install $system_packages
         ;;
     cpan:install)
-        [ -n "$system_packages" ] && print_shell_command "cpan -i $system_packages"
+        [ -n "$system_packages" ] && print_shell_command cpan -i $system_packages
         ;;
     repology:install)
         if [ -n "$system_packages" ]; then

diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
@@ -509,7 +509,9 @@ else
         # just copy to dist/ and create a simple install script.
         mkdir -p dist
         cp "$PKG_SRC" dist/
-        echo "sdh_store_and_pip_install_wheel ." > spkg-install.in
+        if [ ! -f spkg-install.in ]; then
+            echo "sdh_store_and_pip_install_wheel ." > spkg-install.in
+        fi
         ;;
     *)
         # Source tarball

diff --git a/build/bin/sage-spkg-info b/build/bin/sage-spkg-info
@@ -5,11 +5,26 @@
 #
 #  Assumes SAGE_ROOT is set
 PKG_BASE=$1
+if [ -n "$OUTPUT_DIR" ]; then
+    exec > "$OUTPUT_DIR"/$PKG_BASE.rst
+fi
+if [ -n "$OUTPUT_RST" ]; then
+    echo ".. _spkg_$PKG_BASE:"
+    echo
+    ref ()   { echo ":ref:\`$1\`"; }
+    issue () { echo ":issue:\`$1\`"; }
+    code ()  { echo "\`\`$*\`\`"; }
+else
+    ref ()   { echo "$1"; }
+    issue () { echo "https://github.com/sagemath/sage/issues/$1"; }
+    code ()  { echo "$1"; }
+fi
 PKG_SCRIPTS="$SAGE_ROOT/build/pkgs/$PKG_BASE"
 for ext in rst txt; do
     SPKG_FILE="$PKG_SCRIPTS/SPKG.$ext"
     if [ -f "$SPKG_FILE" ]; then
-        sed "1,3s/^ *Sage: Open Source Mathematics Software:/$PKG_BASE:/" "$SPKG_FILE"
+        # for sphinx 4.4 we need to replace all direct links by some "extlink" (issue 33272)
+        sed -e "1,3s/^ *Sage: Open Source Mathematics Software:/$PKG_BASE:/" -e "s|https://github.com/sagemath/sage/issues/\([0-9]*\)|:issue:\`\1\`|g" -e "s|https://arxiv.org/abs/cs/\([0-9]*\)|:arxiv:\`cs/\1\`|g" "$SPKG_FILE"
         break
     fi
 done
@@ -39,9 +54,9 @@ for dep_file in dependencies dependencies_order_only; do
                 # Dependencies like $(BLAS)
                 \$\(*)      echo "- $dep";;
                 # Looks like a package
-                *)          if [ -n "$OUTPUT_RST" -a -r "$SAGE_ROOT/build/pkgs/$dep/SPKG.rst" ]; then
+                *)          if [ -r "$SAGE_ROOT/build/pkgs/$dep/SPKG.rst" ]; then
                                 # This RST label is set in src/doc/bootstrap
-                                echo "- :ref:\`spkg_$dep\`"
+                                echo "- $(ref spkg_$dep)"
                             else
                                 echo "- $dep"
                             fi;;
@@ -103,7 +118,7 @@ for system in $systems; do
                 echo "$system:"
                 ;;
         esac
-        sage-print-system-package-command $system --prompt='    $ ' --sudo install $system_packages
+        sage-print-system-package-command $system --wrap --prompt='    $ ' --continuation='          ' --sudo install $system_packages
         echo
 done
 if [ -z "$system" ]; then
@@ -114,15 +129,15 @@ else
     if [ -f "${SPKG_CONFIGURE}" ]; then
         if grep -q SAGE_PYTHON_PACKAGE_CHECK "${SPKG_CONFIGURE}"; then
             echo "If the system package is installed and if the (experimental) option"
-            echo "--enable-system-site-packages is passed to ./configure, then ./configure"
+            echo "$(code --enable-system-site-packages) is passed to $(code ./configure), then $(code ./configure)"
             echo "will check if the system package can be used."
         else
-            echo "If the system package is installed, ./configure will check if it can be used."
+            echo "If the system package is installed, $(code ./configure) will check if it can be used."
         fi
     else
         echo "However, these system packages will not be used for building Sage"
-        echo "because spkg-configure.m4 has not been written for this package;"
-        echo "see https://github.com/sagemath/sage/issues/27330"
+        echo "because $(code spkg-configure.m4) has not been written for this package;"
+        echo "see $(issue 27330)"
     fi
 fi
 echo
diff --git a/build/bin/write-dockerfile.sh b/build/bin/write-dockerfile.sh
@@ -16,12 +16,15 @@ export PATH="$SAGE_ROOT"/build/bin:$PATH
 SYSTEM_PACKAGES=$EXTRA_SYSTEM_PACKAGES
 CONFIGURE_ARGS="--enable-option-checking "
 for SPKG in $(sage-package list --has-file=spkg-configure.m4 $SAGE_PACKAGE_LIST_ARGS) $EXTRA_SAGE_PACKAGES; do
-    SYSTEM_PACKAGE=$(sage-get-system-packages $SYSTEM $SPKG | sed 's/${PYTHON_MINOR}/'${PYTHON_MINOR}'/g')
+    SYSTEM_PACKAGE=$(sage-get-system-packages $SYSTEM $SPKG)
     if [ -n "${SYSTEM_PACKAGE}" ]; then
-	# SYSTEM_PACKAGE can be empty if, for example, the environment
-	# variable ENABLE_SYSTEM_SITE_PACKAGES is empty.
-	SYSTEM_PACKAGES+=" ${SYSTEM_PACKAGE}"
-	CONFIGURE_ARGS+="--with-system-${SPKG}=${WITH_SYSTEM_SPKG} "
+        # SYSTEM_PACKAGE can be empty if, for example, the environment
+        # variable ENABLE_SYSTEM_SITE_PACKAGES is empty.
+        for a in $SYSTEM_PACKAGE; do
+            # shell-quote package if necessary
+            SYSTEM_PACKAGES+=$(printf " %q" "$a")
+        done
+        CONFIGURE_ARGS+="--with-system-${SPKG}=${WITH_SYSTEM_SPKG} "
     fi
 done
 echo "# Automatically generated by SAGE_ROOT/build/bin/write-dockerfile.sh"

diff --git a/build/make/Makefile.in b/build/make/Makefile.in
@@ -324,7 +324,7 @@ all-toolchain: base-toolchain
 
 # Shorthand for a list of packages sufficient for building and installing
 # typical Python packages from source. Wheel packages only need pip.
-PYTHON_TOOLCHAIN = setuptools pip setuptools_scm wheel setuptools_wheel
+PYTHON_TOOLCHAIN = setuptools pip setuptools_scm wheel flit_core hatchling
 
 # Trac #32056: Avoid installed setuptools leaking into the build of python3 by uninstalling it.
 # It will have to be reinstalled anyway because of its dependency on $(PYTHON).

diff --git a/build/pkgs/_bootstrap/distros/arch.txt b/build/pkgs/_bootstrap/distros/arch.txt
@@ -1,3 +1,5 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool
+autoconf
+automake
+libtool
 pkgconf
diff --git a/build/pkgs/_bootstrap/distros/cygwin.txt b/build/pkgs/_bootstrap/distros/cygwin.txt
@@ -1,2 +1,4 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool
+autoconf
+automake
+libtool
diff --git a/build/pkgs/_bootstrap/distros/fedora.txt b/build/pkgs/_bootstrap/distros/fedora.txt
@@ -1,4 +1,5 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool
-# Fedora 26 needs:
+autoconf
+automake
+libtool
 pkg-config
diff --git a/build/pkgs/_bootstrap/distros/freebsd.txt b/build/pkgs/_bootstrap/distros/freebsd.txt
@@ -1,2 +1,5 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool pkg-config
+autoconf
+automake
+libtool
+pkg-config
diff --git a/build/pkgs/_bootstrap/distros/homebrew.txt b/build/pkgs/_bootstrap/distros/homebrew.txt
@@ -1,2 +1,5 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool pkg-config
+autoconf
+automake
+libtool
+pkg-config
diff --git a/build/pkgs/_bootstrap/distros/macports.txt b/build/pkgs/_bootstrap/distros/macports.txt
@@ -0,0 +1,6 @@
+# Packages needed for ./bootstrap
+gettext
+autoconf
+automake
+libtool
+pkgconfig
diff --git a/build/pkgs/_bootstrap/distros/nix.txt b/build/pkgs/_bootstrap/distros/nix.txt
@@ -1,2 +1,5 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool pkg-config
+autoconf
+automake
+libtool
+pkg-config
diff --git a/build/pkgs/_bootstrap/distros/void.txt b/build/pkgs/_bootstrap/distros/void.txt
@@ -1,4 +1,7 @@
 # Packages needed for ./bootstrap
-autoconf automake libtool
-xtools mk-configure
+autoconf
+automake
+libtool
+xtools
+mk-configure
 pkg-config
diff --git a/build/pkgs/_prereq/distros/alpine.txt b/build/pkgs/_prereq/distros/alpine.txt
@@ -1,3 +1,12 @@
+# This file, build/pkgs/_prereq/distros/alpine.txt, contains names of
+# Alpine Linux packages needed for installation of Sage from source.
+#
+# In addition, the files build/pkgs/SPKG/distros/alpine.txt contain
+# the names of packages that provide the equivalent of SPKG.
+#
+# One package per line. No need to escape special characters.
+# Everything on a line after a # character is ignored.
+#
 binutils
 make
 m4

diff --git a/build/pkgs/_prereq/distros/arch.txt b/build/pkgs/_prereq/distros/arch.txt
@@ -1,3 +1,12 @@
+# This file, build/pkgs/_prereq/distros/arch.txt, contains names of
+# Arch Linux packages needed for installation of Sage from source.
+#
+# In addition, the files build/pkgs/SPKG/distros/arch.txt contain
+# the names of packages that provide the equivalent of SPKG.
+#
+# One package per line. No need to escape special characters.
+# Everything on a line after a # character is ignored.
+#
 binutils
 make
 m4