Merge branch 'develop' into normaliz_3_10

.devcontainer/portability-updateContent.sh

@@ -5,14 +5,14 @@
 # The script assumes that it is run from SAGE_ROOT.
 #
 # If "config.log" or "logs" are symlinks (for example, created by 'tox -e local-...',
-# or after https://trac.sagemath.org/ticket/33262), they might point outside of
+# or after https://github.com/sagemath/sage/issues/33262), they might point outside of
 # the dev container, so remove them. Likewise for upstream.
 for f in config.log logs upstream; do
     if [ -L $f ]; then
         rm -f $f
     fi
 done
-# If possible (ensured after https://trac.sagemath.org/ticket/33262), keep the
+# If possible (ensured after https://github.com/sagemath/sage/issues/33262), keep the
 # logs in the container.
 if [ ! -d logs ]; then
     ln -s /sage/logs logs

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci-macos.yml

@@ -38,7 +38,7 @@ jobs:
       matrix:
         stage: ["1", "2", "2-optional-0-o", "2-optional-p-z", "2-experimental-0-o", "2-experimental-p-z"]
         # python3_xcode is only accepted if enough packages are available from the system
-        # --> to test "minimal", we would need https://trac.sagemath.org/ticket/30949
+        # --> to test "minimal", we would need https://github.com/sagemath/sage/issues/30949
         tox_env: [homebrew-macos-usrlocal-minimal, homebrew-macos-usrlocal-standard, homebrew-macos-usrlocal-maximal, homebrew-macos-usrlocal-python3_xcode-standard, conda-forge-macos-minimal, conda-forge-macos-standard, conda-forge-macos-maximal]
         xcode_version_factor: [default]
         os: [ macos-11, macos-12 ]

.github/workflows/ci-wsl.yml

@@ -13,7 +13,7 @@ jobs:
   windows:
     runs-on: windows-latest
     name: Ubuntu 20.04
-    # Following https://trac.sagemath.org/ticket/25206#comment:63
+    # Following https://github.com/sagemath/sage/issues/25206#comment:63
     steps:
     - name: Configure git
       run: git config --global core.symlinks true

.gitignore

@@ -187,7 +187,7 @@ build/bin/sage-build-env-config
 /pkgs/sagemath-repl/requirements.txt
 /pkgs/sagemath-categories/MANIFEST.in
 
-# same for old locations - before Trac #31577
+# same for old locations - before Issue #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta0", 
-    "version": "10.0.beta0", 
+    "title": "sagemath/sage: 10.0.beta2", 
+    "version": "10.0.beta2", 
     "upload_type": "software", 
-    "publication_date": "2023-02-12", 
+    "publication_date": "2023-02-23", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "/~https://github.com/sagemath/sage/tree/10.0.beta0", 
+            "identifier": "/~https://github.com/sagemath/sage/tree/10.0.beta2", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -31,7 +31,7 @@ SAGE_ROOT_LOGS = logs
 
 # The --stop flag below is just a random flag to induce graceful
 # breakage with non-GNU versions of make.
-# See https://trac.sagemath.org/ticket/24617
+# See https://github.com/sagemath/sage/issues/24617
 
 # Defer unknown targets to build/make/Makefile
 %::
@@ -259,8 +259,8 @@ TEST_FILES = --all
 TEST_FLAGS =
 
 # When the documentation is installed, "optional" also includes all tests marked 'sagemath_doc_html',
-# see https://trac.sagemath.org/ticket/25345, https://trac.sagemath.org/ticket/26110, and
-# https://trac.sagemath.org/ticket/32759
+# see https://github.com/sagemath/sage/issues/25345, https://github.com/sagemath/sage/issues/26110, and
+# https://github.com/sagemath/sage/issues/32759
 TEST_OPTIONAL = sage,optional
 
 # Keep track of the top-level *test* Makefile target for logging.

README.md

@@ -329,7 +329,7 @@ in the Installation Guide.
     manager.
 
     For a large [list of Sage
-    packages](https://trac.sagemath.org/ticket/27330), Sage is able to
+    packages](https://github.com/sagemath/sage/issues/27330), Sage is able to
     detect whether an installed system package is suitable for use with
     Sage; in that case, Sage will not build another copy from source.
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta0, Release Date: 2023-02-12
+SageMath version 10.0.beta2, Release Date: 2023-02-23

bootstrap

@@ -47,17 +47,17 @@ AS_VAR_SET_IF([SAGE_ENABLE_$pkgname], [], [AS_VAR_SET([SAGE_ENABLE_$pkgname], [y
     done
     # --enable-SPKG options
     for pkgname in $(sage-package list :optional: :experimental: | sort); do
-                # Trac #29629: Temporary solution for Sage 9.1: Do not provide
+                # Issue #29629: Temporary solution for Sage 9.1: Do not provide
                 # --enable-SPKG options for installing pip packages
                 if [ ! -f build/pkgs/$pkgname/requirements.txt ]; then
                     pkgtype="$(cat build/pkgs/$pkgname/type)"
-                    # Trac #29124: Do not provide --enable-_recommended and similar
+                    # Issue #29124: Do not provide --enable-_recommended and similar
                     case "$pkgname" in
                         _*) ;;
                         *)  spkg_configures="$spkg_configures
 AC_SUBST(SAGE_ENABLE_$pkgname, [if_installed])"
                             if [ -f build/pkgs/$pkgname/spkg-install -o -f build/pkgs/$pkgname/spkg-install.in ]; then
-                                # Trac #31163: Not just an optional dummy package
+                                # Issue #31163: Not just an optional dummy package
                                 spkg_configures="$spkg_configures
 SAGE_SPKG_ENABLE([$pkgname], [$pkgtype], [$(grep -v ^= build/pkgs/$pkgname/SPKG.rst | head -n1 2>/dev/null || echo $pkgname)])"
                             fi

build/bin/sage-bootstrap-python

@@ -30,7 +30,7 @@ SAGE_ORIG_PATH=${NEW_PATH%%':'}
 # Also, Trac #20023 removed the vendored argparse library from sage_bootstrap,
 # so we test that python is new enough (>= 2.7) to run it.
 #
-# See https://trac.sagemath.org/ticket/29090
+# See https://github.com/sagemath/sage/issues/29090
 
 # Trac #29890: Our first choice is "python", not "python3". This is to avoid
 # a defect of sage_bootstrap on macOS regarding SSL URLs.

build/bin/sage-build-num-threads

@@ -10,7 +10,7 @@
 # 3) The number of CPU cores in the system, as determined by
 #    multiprocessing.cpu_count()
 #
-# AUTHOR: Jeroen Demeyer (2011-12-08): Trac ticket #12016
+# AUTHOR: Jeroen Demeyer (2011-12-08): Github issue #12016
 #
 
 from __future__ import print_function

build/bin/sage-dist-helpers

@@ -98,7 +98,7 @@
 #    (Linux only--no-op on other platforms.)  Check shared libraries loaded by
 #    EXECUTABLE (may be a program or another library) for a library starting
 #    with SONAME, and if found appends SONAME to the LD_PRELOAD environment
-#    variable.  See https://trac.sagemath.org/24885.
+#    variable.  See https://github.com/sagemath/sage/issues/24885.
 
 set -o allexport
 
@@ -166,7 +166,7 @@ sdh_configure() {
     echo "Configuring $PKG_NAME"
     # Run all configure scripts with bash to work around bugs with
     # non-portable scripts.
-    # See https://trac.sagemath.org/ticket/24491
+    # See https://github.com/sagemath/sage/issues/24491
     if [ -z "$CONFIG_SHELL" ]; then
         export CONFIG_SHELL=`command -v bash`
     fi
@@ -290,7 +290,7 @@ sdh_pip_install() {
 
 sdh_pip_editable_install() {
     echo "Installing $PKG_NAME (editable mode)"
-    # Until https://trac.sagemath.org/ticket/34209 switches us to PEP 660 editable wheels
+    # Until https://github.com/sagemath/sage/issues/34209 switches us to PEP 660 editable wheels
     export SETUPTOOLS_ENABLE_FEATURES=legacy-editable
     python3 -m pip install --verbose --no-deps --no-index --no-build-isolation --isolated --editable "$@" || \
         sdh_die "Error installing $PKG_NAME"

build/bin/sage-flock

@@ -11,7 +11,7 @@
 # This is originally motivated by pip, but has since been generalized.  We
 # should avoid running pip while uninstalling a package because that is prone
 # to race conditions. This script can be used to run pip under a lock.  For
-# details, see https://trac.sagemath.org/ticket/21672
+# details, see https://github.com/sagemath/sage/issues/21672
 
 try:
     import sage_bootstrap

build/bin/sage-site

@@ -184,7 +184,7 @@ if [ "$1" = '-i' ]; then
     for PKG in $PACKAGES; do
         echo
         # Check that $PKG is actually a Makefile target
-        # See https://trac.sagemath.org/ticket/25078
+        # See https://github.com/sagemath/sage/issues/25078
         if ! echo "$ALL_TARGETS" | grep "^${PKG}$" >/dev/null; then
             echo >&2 "Error: package '$PKG' not found"
             echo >&2 "Note: if it is an old-style package, installing these is no longer supported"

build/bin/sage-spkg

@@ -686,7 +686,7 @@ echo "Copying package files from temporary location $SAGE_DESTDIR to $SAGE_INST_
 if [ -d "$SAGE_DESTDIR" ]; then
     # Some `find` implementations will put superfluous slashes in the
     # output if we give them a directory name with a slash; so make sure
-    # any trailing slash is removed; https://trac.sagemath.org/ticket/26013
+    # any trailing slash is removed; https://github.com/sagemath/sage/issues/26013
     PREFIX="${SAGE_DESTDIR_LOCAL%/}"
 
     rm -f "$PREFIX"/lib/*.la

build/bin/sage-spkg-info

@@ -116,10 +116,10 @@ else
         echo "However, these system packages will not be used for building Sage"
         if [ -f "$PKG_SCRIPTS"/install-requires.txt ]; then
             echo "because using Python site-packages is not supported by the Sage distribution;"
-            echo "see https://trac.sagemath.org/ticket/29023"
+            echo "see https://github.com/sagemath/sage/issues/29023"
         else
             echo "because spkg-configure.m4 has not been written for this package;"
-            echo "see https://trac.sagemath.org/ticket/27330"
+            echo "see https://github.com/sagemath/sage/issues/27330"
         fi
     fi
 fi

build/bin/sage-venv

@@ -38,7 +38,7 @@ if options.upgrade and options.clear:
     raise ValueError('you cannot supply --upgrade and --clear together.')
 
 if sys.platform == 'cygwin':
-    # default for Cygwin; see https://trac.sagemath.org/ticket/30149
+    # default for Cygwin; see https://github.com/sagemath/sage/issues/30149
     use_symlinks = False
 else:
     # default for posix

build/make/Makefile.in

@@ -78,7 +78,7 @@ DUMMY_PACKAGES = @SAGE_DUMMY_PACKAGES@
 
 # Set to the path to Sage's GCC (if GCC is installed) to force rebuilds
 # of packages if GCC changed.
-# See m4/sage_spkg_collect.m4 and https://trac.sagemath.org/ticket/24703
+# See m4/sage_spkg_collect.m4 and https://github.com/sagemath/sage/issues/24703
 GCC_DEP = @SAGE_GCC_DEP@
 
 # Versions of all the packages, in the format

build/pkgs/_prereq/distros/cygwin.txt

@@ -12,14 +12,14 @@
 binutils
 make
 m4
-# a system python is needed for downloading the sage packages, https://trac.sagemath.org/ticket/29090
+# a system python is needed for downloading the sage packages, https://github.com/sagemath/sage/issues/29090
 python39-urllib3 python39
 perl
 perl-ExtUtils-MakeMaker
 tar
 gcc-core
 gcc-g++
-# Needed according to embray at https://trac.sagemath.org/ticket/26964:
+# Needed according to embray at https://github.com/sagemath/sage/issues/26964:
 # The need for which comes [...] from MPIR's configure script
 findutils
 which

build/pkgs/_prereq/distros/fedora.txt

@@ -15,7 +15,7 @@
 binutils
 make
 m4
-# a system python is needed for downloading the sage packages, https://trac.sagemath.org/ticket/29090
+# a system python is needed for downloading the sage packages, https://github.com/sagemath/sage/issues/29090
 python3
 perl
 perl-ExtUtils-MakeMaker
@@ -26,11 +26,11 @@ gcc
 # configure: error: in `/sage':
 # configure: error: C++ preprocessor "/lib/cpp" fails sanity check
 gcc-c++
-# Needed according to embray at https://trac.sagemath.org/ticket/26964:
+# Needed according to embray at https://github.com/sagemath/sage/issues/26964:
 # The need for which comes [...] from MPIR's configure script
 findutils
 which
-# Needed for pcre configure, see https://trac.sagemath.org/ticket/29129:
+# Needed for pcre configure, see https://github.com/sagemath/sage/issues/29129:
 diffutils
 # Needed for openssl 3.0
 perl-IPC-Cmd

build/pkgs/cddlib/spkg-configure.m4

@@ -16,7 +16,7 @@ SAGE_SPKG_CONFIGURE([cddlib], [
     AC_CHECK_PROGS(SCDD, [scdd_gmp scdd])
     AS_IF([test x$SCDD = x], [sage_spkg_install_cddlib=yes])
 
-    dnl https://trac.sagemath.org/ticket/30319
+    dnl https://github.com/sagemath/sage/issues/30319
     AS_IF([test -n "$CDDEXEC"], [
         AC_MSG_CHECKING([whether $CDDEXEC --redcheck works correctly for real input])
         cat > conftest.ine <<EOF

build/pkgs/cmake/spkg-check.in

@@ -1,8 +1,8 @@
-# Do not run a test suite: see https://trac.sagemath.org/ticket/30093.
+# Do not run a test suite: see https://github.com/sagemath/sage/issues/30093.
 #
 # - The test suite takes a long time and can fail in minor ways.
 # - If some major aspect of cmake fails, it only affects the build
 #   process of Sage, not the mathematical correctness of its results.
 # - If some minor aspect of cmake fails, it won't affect anything about Sage.
 
-echo "We skip the test suite for cmake: see https://trac.sagemath.org/ticket/30093."
+echo "We skip the test suite for cmake: see https://github.com/sagemath/sage/issues/30093."

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=fc9c71ad5be4e3197007ddb150cba47d15716d89
-md5=0a707bcc4316b8c3e3faca6330fc5dc2
-cksum=3972886119
+sha1=a9dd38e83511f7f7911c94366c1c7b9e213cea3e
+md5=e341828a3c4d17b37887cd93c298286f
+cksum=2811082803

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-785ddef6338073b27082bb675446e3ae111b3b5d
+bbd91d34c346cbb308e6bfac72ac414b365f190c

build/pkgs/curl/spkg-check.in

@@ -1,8 +1,8 @@
-# Do not run a test suite: see https://trac.sagemath.org/ticket/30093.
+# Do not run a test suite: see https://github.com/sagemath/sage/issues/30093.
 #
 # - The test suite takes a long time and can fail in minor ways.
 # - If some major aspect of curl fails, it only affects the build
 #   process of Sage, not the mathematical correctness of its results.
 # - If some minor aspect of curl fails, it won't affect anything about Sage.
 
-echo "We skip the test suite for curl: see https://trac.sagemath.org/ticket/30093."
+echo "We skip the test suite for curl: see https://github.com/sagemath/sage/issues/30093."

build/pkgs/ecl/SPKG.rst

@@ -43,7 +43,7 @@ Special Update/Build Instructions
 
 -  Do NOT quote SAGE_LOCAL when setting CPPFLAGS and/or LDFLAGS,
    in spkg-install as this caused the build to break. See
-   http://trac.sagemath.org/sage_trac/ticket/10187#comment:117
+   :issue:`10187#comment:117`
 
 -  TODO: Add the ECL test suite, and an spkg-check file to run it.
 -  TODO: Make ECL use Sage's Boehm GC on MacOS X as well (but perhaps

build/pkgs/ecl/spkg-install.in

@@ -2,7 +2,7 @@ cd src
 
 if [ "$UNAME" = "CYGWIN" ]; then
     # Some of ECL's sources rely on GNU-isms that are allowed by default on
-    # most glibcs, but not in newlib; https://trac.sagemath.org/ticket/25057
+    # most glibcs, but not in newlib; https://github.com/sagemath/sage/issues/25057
     CFLAGS="$CFLAGS -D_GNU_SOURCE"
     CXXFLAGS="$CXXFLAGS -D_GNU_SOURCE"
 fi

build/pkgs/ecm/spkg-install.in

@@ -92,10 +92,10 @@ else
             # Don't add debug symbols because configure otherwise
             # fails due to a bus error in Apple's 'ld' when trying
             # to determine if global symbols are prefixed with an
-            # underscore (cf. http://trac.sagemath.org/sage_trac/ticket/5847#comment:35 ff.):
+            # underscore (cf. https://github.com/sagemath/sage/issues/5847#comment:35 ff.):
             echo >&2 "Warning: Disabling debug symbols on MacOS X 10.5" \
                 "PowerPC because of a linker (?) bug."
-            echo >&2 "See http://trac.sagemath.org/sage_trac/ticket/5847#comment:35" \
+            echo >&2 "See https://github.com/sagemath/sage/issues/5847#comment:35" \
                 "ff. for details."
             echo >&2
             CFLAGS="-O3 $ORIGINAL_CFLAGS"

build/pkgs/elliptic_curves/spkg-install.py

@@ -60,7 +60,7 @@ def install_ellcurves():
     ellcurves_root = os.path.join(SAGE_SHARE, 'ellcurves')
 
     # Remove previous installs (possibly with bad permissions, see
-    # https://trac.sagemath.org/ticket/21641)
+    # https://github.com/sagemath/sage/issues/21641)
     import shutil
     try:
         shutil.rmtree(ellcurves_root)

build/pkgs/fflas_ffpack/spkg-install.in

@@ -24,13 +24,13 @@ if [ "$SAGE_FAT_BINARY" = yes ]; then
 fi
 
 # Need to use 'bash' for configure, see
-# https://trac.sagemath.org/ticket/23451
+# https://github.com/sagemath/sage/issues/23451
 if [ -z "$CONFIG_SHELL" ]; then
     export CONFIG_SHELL=`command -v bash`
 fi
 
 # We disable openmp because of build failures, see
-# http://trac.sagemath.org/ticket/17635#comment:67
+# https://github.com/sagemath/sage/issues/17635#comment:67
 sdh_configure --with-default="$SAGE_LOCAL" --with-blas-libs="$LINBOX_BLAS" \
               "$LINBOX_BLAS_CFLAGS" --disable-static \
               --enable-precompilation $FFLAS_FFPACK_CONFIGURE

build/pkgs/gap/spkg-install.in

@@ -53,7 +53,7 @@ sdh_install pkg/GAPDoc-* pkg/primgrp-* pkg/SmallGrp-* pkg/transgrp "$GAP_ROOT"/p
 # typically "expected" to be loaded: These are the default packages that are
 # autoloaded at GAP startup (via the PackagesToLoad UserPreference) with an
 # out-of-the-box GAP installation; see
-# https://trac.sagemath.org/ticket/22626#comment:393 for discussion on this
+# https://github.com/sagemath/sage/issues/22626#comment:393 for discussion on this
 #
 # Also include atlasrep which is a dependency of tomlib
 sdh_install \
@@ -96,7 +96,7 @@ done
 # be going away.  This breaks the build toolchain for some compiled GAP
 # packages.  We need to replace these paths with the final GAP_ROOT path.  The
 # below will work so long as neither of these paths contain '|', and if they do
-# then god help you.  https://trac.sagemath.org/ticket/27218
+# then god help you.  https://github.com/sagemath/sage/issues/27218
 sed -i -e "s|$GAP_BUILD_ROOT|$GAP_ROOT|g" \
     "$SAGE_DESTDIR$SAGE_BIN/gac" "$DESTDIR_GAP_ROOT/sysinfo.gap" \
     "$DESTDIR_GAP_ROOT/bin/gap.sh" "$DESTDIR_GAP_ROOT/doc/make_doc" || \