Merge #32733

.homebrew-build-env

@@ -2,7 +2,7 @@
 # that activate keg-only homebrew package installations
 
 HOMEBREW=`brew --prefix` || return 1
-for l in gettext bzip2 texinfo; do
+for l in gettext bzip2 texinfo polymake; do
     if [ -d "$HOMEBREW/opt/$l/bin" ]; then
         PATH="$HOMEBREW/opt/$l/bin:$PATH"
     fi
@@ -23,7 +23,7 @@ export PKG_CONFIG_PATH
 LIBRARY_PATH="$HOMEBREW/lib$LIBRARY_PATH"
 [ -z "$CPATH" ] || CPATH=":${CPATH}"
 CPATH="$HOMEBREW/include$CPATH"
-for l in readline bzip2 ntl; do
+for l in readline bzip2 ntl polymake; do
     if [ -d "$HOMEBREW/opt/$l/lib" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l/lib:$LIBRARY_PATH"
     fi

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta5", 
-    "version": "9.5.beta5", 
+    "title": "sagemath/sage: 9.5.beta6", 
+    "version": "9.5.beta6", 
     "upload_type": "software", 
-    "publication_date": "2021-10-28", 
+    "publication_date": "2021-11-12", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta5", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta6", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.beta5, Release Date: 2021-10-28
+SageMath version 9.5.beta6, Release Date: 2021-11-12

build/bin/sage-dist-helpers

@@ -56,11 +56,12 @@
 #    be given as arguments.  If $SAGE_DESTDIR is not set then the command is
 #    run with $SAGE_SUDO, if set.
 #
-# - sdh_pip_install [...]
+# - sdh_pip_install [--no-deps] [--build-isolation] [...]
 #
-#    Runs `pip install` with the given arguments, as well as additional
-#    default arguments used for installing packages into Sage with pip.
-#    Currently this is just a wrapper around the `sage-pip-install` command.
+#    Builds a wheel using `pip wheel` with the given options [...], then installs
+#    the wheel.  Unless the special option --build-isolation is given,
+#    the wheel is built using the option --no-build-isolation.
+#    If the special option --no-deps is given, it is passed to pip install.
 #    If $SAGE_DESTDIR is not set then the command is run with $SAGE_SUDO, if
 #    set.
 #
@@ -240,10 +241,31 @@ sdh_pip_install() {
     echo "Installing $PKG_NAME"
     mkdir -p dist
     rm -f dist/*.whl
-    python3 -m pip wheel --use-feature=in-tree-build --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation --ignore-requires-python "$@" || \
+    install_options=""
+    # pip has --no-build-isolation but no flag that turns the default back on...
+    build_isolation_option="--no-build-isolation --no-binary :all:"
+    while [ $# -gt 0 ]; do
+        case "$1" in
+            --build-isolation)
+                # If a package requests build isolation, we allow it to provision
+                # its build environment using the stored wheels.
+                # We pass --find-links and remove the --no-binary option.
+                # The SPKG needs to declare "setuptools_wheel" as a dependency.
+                build_isolation_option="--find-links=$SAGE_SPKG_WHEELS"
+                ;;
+            --no-deps)
+                install_options="$install_options $1"
+                ;;
+            *)
+                break
+                ;;
+        esac
+        shift
+    done
+    python3 -m pip wheel --use-feature=in-tree-build --wheel-dir=dist --verbose --no-deps --no-index --isolated --ignore-requires-python $build_isolation_option "$@" || \
         sdh_die "Error building a wheel for $PKG_NAME"
 
-    sdh_store_and_pip_install_wheel .
+    sdh_store_and_pip_install_wheel $install_options .
 }
 
 sdh_store_wheel() {

build/bin/sage-spkg

@@ -498,15 +498,14 @@ export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"
 export PKG_VER="$PKG_VER"
 
-for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env-config" "\$SAGE_SRC/bin/sage-env" "\$SAGE_ROOT/build/bin/sage-build-env-config" "\$SAGE_ROOT/build/bin/sage-build-env"; do
+for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-src-env-config" "\$SAGE_SRC/bin/sage-env-config" "\$SAGE_SRC/bin/sage-env" "\$SAGE_ROOT/build/bin/sage-build-env-config" "\$SAGE_ROOT/build/bin/sage-build-env"; do
     source "\$lib"
     if [ \$? -ne 0 ]; then
         echo >&2 "Error: failed to source \$lib"
         echo >&2 "Is \$SAGE_ROOT the correct SAGE_ROOT?"
         exit 1
     fi
 done
-export PATH="$SAGE_INST_LOCAL/bin:$PATH"
 
 export SAGE_INST_LOCAL="$SAGE_INST_LOCAL"
 
@@ -773,6 +772,7 @@ if [ "$SAGE_CHECK" = "yes" -o "$SAGE_CHECK" = "warn" ]; then
         if [ $? -ne 0 ]; then
             TEST_SUITE_RESULT="failed"
             if [ "$SAGE_CHECK" = "warn" ]; then
+                # The following warning message must be consistent with SAGE_ROOT/build/make/install (see trac:32781)
                 error_msg "Warning: Failures testing package $PKG_NAME (ignored)" "make check"
             else
                 error_msg "Error testing package $PKG_NAME" "make check"

build/make/install

@@ -122,7 +122,8 @@ EOF
 
 elif [ "$SAGE_CHECK" = "warn" ]; then
     echo "SAGE_CHECK=warn, so scanning the log files. This may take a few seconds."
-    warnings=`look_for_errors "$SAGE_LOGS/*.log" 20 "^Warning: Error testing" package`
+    # The following warning message must be consistent with SAGE_ROOT/build/bin/sage-spkg (see trac:32781)
+    warnings=`look_for_errors "$SAGE_LOGS/*.log" 20 "^Warning: Failures testing package" package`
     if [ -n "$warnings" ]; then
         cat >&2 <<EOF
 ***************************************************************

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=ab6592f2216c48049bbbcfb3a42c3e157f44d917
-md5=fc3a50e0f47802e55969eade44648af4
-cksum=3704729867
+sha1=bdfd5753a2548365230216455d9a543fe238f092
+md5=49ffa01e32a876dd4feea975d822351e
+cksum=3517586928

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-c5a87834e7e2939b878a5134cd240e6c712bd573
+fda367752b5e7afa3ec0fda483b162645192e008

build/pkgs/database_knotinfo/checksums.ini

@@ -1,5 +1,5 @@
 tarball=database_knotinfo-VERSION.tar.gz
-sha1=549e3162b2ba6942dede30366072d10e26643f54
-md5=c6487321cd2e0fd6b9f9ee7bdfa19993
-cksum=2255768788
+sha1=187e6b5ee2a935e3a50bc7648b181dfc7cb7bfa2
+md5=90822e09a1a84c8dbb84e20773c367f1
+cksum=1855405219
 upstream_url=https://pypi.io/packages/source/d/database_knotinfo/database_knotinfo-VERSION.tar.gz

build/pkgs/database_knotinfo/package-version.txt

@@ -1 +1 @@
-2021.9.1
+2021.10.1

build/pkgs/gengetopt/SPKG.rst

@@ -0,0 +1,15 @@
+gengetopt: getopt_long parser generator
+===========================================
+
+Description
+-----------
+
+GNU Gengetopt converts a textual description of your program's
+arguments and options into a getopt_long() parser in C (or C++).
+
+Website: https://www.gnu.org/software/gengetopt/
+
+
+License
+-------
+GPL-3+ (https://www.gnu.org/software/gengetopt/LICENSE)

build/pkgs/gengetopt/checksums.ini

@@ -0,0 +1,5 @@
+tarball=gengetopt-VERSION.tar.xz
+sha1=0d5979af61a7be309898608803056aeebe3a3657
+md5=ea165d618640dbdecb42ae4491337965
+cksum=3423561524
+upstream_url=ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-VERSION.tar.xz

build/pkgs/gengetopt/dependencies

@@ -0,0 +1,7 @@
+| xz
+
+xz is needed for unpacking the tarball when sage-bootstrap-python is ancient
+
+----------
+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/gengetopt/distros/cygwin.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/distros/debian.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/distros/fedora.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/distros/gentoo.txt

@@ -0,0 +1 @@
+dev-util/gengetopt

build/pkgs/gengetopt/distros/nix.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/distros/repology.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/distros/void.txt

@@ -0,0 +1 @@
+gengetopt

build/pkgs/gengetopt/package-version.txt

@@ -0,0 +1 @@
+2.23

build/pkgs/gengetopt/spkg-build.in

@@ -0,0 +1,11 @@
+cd src
+sdh_configure
+
+# Don't run "make" at the top-level because the documentation build
+# requires the "makeinfo" program. This is a bug that should be fixed
+# in gengetopt-2.24. First build gnulib, then build gengetopt.
+cd gl
+sdh_make
+cd ../src
+sdh_make
+cd ..

build/pkgs/gengetopt/spkg-check.in

@@ -0,0 +1,8 @@
+cd src
+
+# See spkg-build.in for an explanation of this hack.
+cd src
+sdh_make_check
+cd ../tests
+sdh_make_check
+cd ..

build/pkgs/gengetopt/spkg-configure.m4

@@ -0,0 +1,4 @@
+SAGE_SPKG_CONFIGURE([gengetopt], [
+  AC_PATH_PROG(GENGETOPT, gengetopt)
+  AS_IF([test -z "${GENGETOPT}"], [sage_spkg_install_gengetopt=yes])
+])

build/pkgs/gengetopt/spkg-install.in

@@ -0,0 +1,7 @@
+cd src
+
+# Only run "make install" in the src directory to avoid the
+# documentation, which currently (due to a bug) tries to invoke the
+# "makeinfo" program.
+cd src
+sdh_make_install

build/pkgs/gengetopt/type

@@ -0,0 +1 @@
+standard

build/pkgs/gsl/checksums.ini

@@ -1,5 +1,5 @@
 tarball=gsl-VERSION.tar.gz
-sha1=9273164b6bdf60d0577518a1c1310eff6659e3dd
-md5=bda73a3dd5ff2f30b5956764399db6e7
-cksum=1462047518
+sha1=29179db0d746f422bb0ceca2cbda4de107a2c651
+md5=9e47e81caaebcd92b7aca27a5348df74
+cksum=2494121348
 upstream_url=https://ftp.gnu.org/gnu/gsl/gsl-VERSION.tar.gz

build/pkgs/gsl/dependencies

@@ -1,4 +1,4 @@
-$(BLAS)
+$(BLAS) | pkgconf
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/gsl/package-version.txt

@@ -1 +1 @@
-2.6
+2.7

build/pkgs/gsl/spkg-install.in

@@ -1,5 +1,8 @@
 cd src
 
-sdh_configure LIBS="`pkg-config --libs-only-l cblas` -lm"
+sdh_configure LIBS="`pkg-config --libs-only-l cblas` -lm" \
+              LDFLAGS="$LDFLAGS `pkg-config --libs-only-L cblas`" \
+              CPPFLAGS="$CPPFLAGS `pkg-config --cflags-only-I cblas`" \
+              CFLAGS="$CFLAGS `pkg-config --cflags-only-other cblas`"
 sdh_make
 sdh_make_install

build/pkgs/numpy/spkg-install.in

@@ -16,7 +16,11 @@ if [ "$UNAME" = "CYGWIN" ]; then
     export CPPFLAGS="${CPPFLAGS} -D_GNU_SOURCE"
 fi
 
-python3 ../lapack_conf.py
+# Trac #32746: pkg-config omits -I and -L flags that refer to directories
+# that are already on CPATH, LIBRARY_PATH.
+# But our script tries to obtain the list of include_dirs and library_dirs
+# from pkg-config!
+(unset CPATH LIBRARY_PATH; python3 ../lapack_conf.py)
 
 # Make sure that the fortran objects are compiled with -fPIC
 export FFLAGS="$FFLAGS -fPIC"

build/pkgs/openblas/checksums.ini

@@ -1,5 +1,5 @@
 tarball=openblas-VERSION.tar.gz
-sha1=685537a821819ef4dae5901998a57f0eec5bddad
-md5=2ca05b9cee97f0d1a8ab15bd6ea2b747
-cksum=2414941668
+sha1=a9d5ce86908657f002c6566cd8f35fe882709be4
+md5=5cd5df5a1541ad414f5874aaae17730f
+cksum=2075619020
 upstream_url=https://github.com/xianyi/OpenBLAS/archive/vVERSION.tar.gz

build/pkgs/openblas/package-version.txt

@@ -1 +1 @@
-0.3.13
+0.3.18

build/pkgs/openblas/patches/trsv-fix-from-pr-3422.patch

@@ -0,0 +1,26 @@
+From 4b3769823ac865e66eafe7724f95873cca236751 Mon Sep 17 00:00:00 2001
+From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
+Date: Sun, 24 Oct 2021 23:57:06 +0200
+Subject: [PATCH] Revert #3252
+
+---
+ interface/trsv.c | 6 ------
+ 1 file changed, 6 deletions(-)
+
+diff --git a/interface/trsv.c b/interface/trsv.c
+index 6a6e8f8bab..a054d8eeb6 100644
+--- a/interface/trsv.c
++++ b/interface/trsv.c
+@@ -188,12 +188,6 @@ void CNAME(enum CBLAS_ORDER order, enum CBLAS_UPLO Uplo,
+
+   if (n == 0) return;
+
+-  if (incx == 1 && trans == 0 && n < 50) {
+-    buffer = NULL;
+-    (trsv[(trans<<2) | (uplo<<1) | unit])(n, a, lda, x, incx, buffer);
+-    return;  
+-  }
+-
+   IDEBUG_START;
+
+   FUNCTION_PROFILE_START();

build/pkgs/openblas/spkg-install.in

@@ -14,16 +14,29 @@ fi
 
 if [ "x$SAGE_FAT_BINARY" = "xyes" ]; then
     OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE DYNAMIC_ARCH=1"
+    machine=$($CC -dumpmachine)
+    if [[ $machine =~ x86_64-apple-darwin* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=CORE2"
+    elif [[ $os-$machine =~ arm64-apple-darwin* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=VORTEX"
+    elif [[ $machine =~ (x86_64|amd64)-* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=PRESCOTT"
+    elif [[ $machine =~ (i386|i486|i586|i686)-* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=KATMAI"
+    elif [[ $machine =~ (ppc64le|powerpc64le)-* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=POWER8"
+    elif [[ $machine =~ ppc64-* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=POWER6"
+    elif [[ $machine =~ aarch64-* ]]; then
+        OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=ARMV8"
+    fi
 fi
 
 echo "Building OpenBLAS: $MAKE $OPENBLAS_CONFIGURE"
 
 # Ensure USE_TLS=1 ; see https://trac.sagemath.org/ticket/27256
 OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE USE_TLS=1"
 
-# Disable AVX512 for now, see https://trac.sagemath.org/ticket/27961
-OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE NO_AVX512=1"
-
 if ! (sdh_make libs netlib shared $OPENBLAS_CONFIGURE); then
     if [[ $OPENBLAS_CONFIGURE == *"TARGET"* ]]; then
         sdh_die "Error building OpenBLAS"

build/pkgs/packaging/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | setuptools pip wheel pyparsing
+$(PYTHON) | setuptools pip wheel pyparsing setuptools_wheel
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/packaging/spkg-install.in

@@ -1 +1 @@
-cd src && sdh_pip_install .
+cd src && sdh_pip_install --build-isolation .

build/pkgs/pdf2svg/SPKG.rst

@@ -0,0 +1,19 @@
+pdf2svg - PDF to SVG convertor
+==============================
+
+Description
+-----------
+
+pdf2svg is a tiny command-line utility using Cairo and Poppler to convert PDF
+documents into SVG files. Multi-page PDF can be split up to one SVG per page by
+passing a file naming specification.
+
+License
+-------
+
+GPL
+
+Upstream Contact
+----------------
+
+http://cityinthesky.co.uk/opensource/pdf2svg/

build/pkgs/pdf2svg/distros/alpine.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/arch.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/conda.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/cygwin.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/debian.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/fedora.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/freebsd.txt

@@ -0,0 +1 @@
+graphics/pdf2svg

build/pkgs/pdf2svg/distros/homebrew.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/macports.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/nix.txt

@@ -0,0 +1 @@
+pdf2svg

build/pkgs/pdf2svg/distros/opensuse.txt

@@ -0,0 +1 @@
+pdf2svg