Merge branch 't/31228/the___march_native__flag_vs__the_compiler_used_…

…when_python_extensions_are_built' into t/31227/accept__usr_bin_python3_from_xcode_12_3_on_macos_10_15__catalina_

.github/workflows/lint.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Install pycodestyle
       run: pip install tox pycodestyle
     - name: Lint using pycodestyle
-      run: tox -e pycodestyle
+      run: tox -e pycodestyle-minimal
   lint-relint:
     name: Code style check with relint
     runs-on: ubuntu-latest
@@ -27,7 +27,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
-    - name: Install pycodestyle
+    - name: Install relint
       run: pip install tox relint
     - name: Lint using relint
       run: tox -e relint src/

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta5", 
-    "version": "9.3.beta5", 
+    "title": "sagemath/sage: 9.3.beta6", 
+    "version": "9.3.beta6", 
     "upload_type": "software", 
-    "publication_date": "2020-12-27", 
+    "publication_date": "2021-01-17", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta5", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta6", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -220,9 +220,11 @@ install: all
 	@echo "from https://github.com/sagemath/binary-pkg"
 	@echo "******************************************************************"
 
+# Setting SAGE_PKGCONFIG is only so that make does not exit with
+# "This Makefile needs to be invoked by build/make/install".
 list:
 	@$(MAKE) --silent build/make/Makefile >&2
-	@$(MAKE) --silent -f build/make/Makefile SAGE_SPKG_INST=local $@
+	@$(MAKE) --silent -f build/make/Makefile SAGE_PKGCONFIG=dummy $@
 
 .PHONY: default build dist install micro_release \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \

README.md

@@ -328,8 +328,9 @@ version that you are installing.
 Please do not hesitate to ask for help in the [SageMath forum
 ](https://ask.sagemath.org/questions/) or the [sage-support mailing
 list](https://groups.google.com/forum/#!forum/sage-support).  The
-[Troubleshooting section in the Sage Installation Guide]() provides
-instructions on what information to provide so that we can provide
+[Troubleshooting section in the Sage Installation Guide
+](https://doc.sagemath.org/html/en/installation/troubles.html)
+provides instructions on what information to provide so that we can provide
 help more effectively.
 
 Contributing to Sage

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.beta5, Release Date: 2020-12-27
+SageMath version 9.3.beta6, Release Date: 2021-01-17

build/bin/sage-dist-helpers

@@ -148,7 +148,7 @@ _EOF_
 
 
 sdh_guard() {
-    sdh_check_vars SAGE_ROOT SAGE_LOCAL SAGE_SHARE
+    sdh_check_vars SAGE_ROOT SAGE_LOCAL SAGE_INST_LOCAL SAGE_SHARE
 }
 
 
@@ -160,9 +160,9 @@ sdh_configure() {
     if [ -z "$CONFIG_SHELL" ]; then
         export CONFIG_SHELL=`command -v bash`
     fi
-    ./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" --disable-maintainer-mode --disable-dependency-tracking "$@"
+    ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" --disable-maintainer-mode --disable-dependency-tracking "$@"
     if [ $? -ne 0 ]; then # perhaps it is a non-autoconf'd project
-      ./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" "$@"
+      ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" "$@"
       if [ $? -ne 0 ]; then
         if [ -f "$(pwd)/config.log" ]; then
             sdh_die <<_EOF_
@@ -261,7 +261,7 @@ sdh_store_and_pip_install_wheel() {
 
 sdh_cmake() {
     echo "Configuring $PKG_NAME with cmake"
-    cmake . -DCMAKE_INSTALL_PREFIX="${SAGE_LOCAL}" \
+    cmake . -DCMAKE_INSTALL_PREFIX="${SAGE_INST_LOCAL}" \
             -DCMAKE_INSTALL_LIBDIR=lib \
             "$@"
     if [ $? -ne 0 ]; then

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

@@ -119,6 +119,9 @@ case $system:$command in
     freebsd*:install)
         [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}pkg install $system_packages"
         ;;
+    nix*:install)
+        [ -n "$system_packages" ] && echo "${PROMPT}nix-env --install $system_packages"
+        ;;
     pip:install)
         [ -n "$system_packages" ] && echo "${PROMPT}sage -pip install $system_packages"
         ;;

build/bin/sage-sdist

@@ -2,7 +2,8 @@
 
 ########################################################
 # Build Sage source distribution
-# This script should be called by the spkg/bin/sage script
+# This script should not be invoked directly.
+# Use "sage --sdist" or "make dist".
 ########################################################
 
 set -e

build/bin/sage-spkg

@@ -5,6 +5,10 @@
 #  This script is typically invoked by giving the command
 #      sage {-i|-p} <options> <package name>...
 #
+#  sage-spkg itself only accepts one <package name>.
+#
+#      sage-spkg <options> <package name> [<installation tree>]
+#
 #  Options can be:
 #   -s: do not delete temporary build directory
 #   -k: do not uninstall existing installation of this package before
@@ -24,8 +28,11 @@
 #  A package may assume that the following environment
 #  variables are defined:
 #
-#      SAGE_ROOT      -- root directory of sage install
-#      SAGE_LOCAL     -- $SAGE_ROOT/local
+#      SAGE_ROOT      -- root directory of sage distribution
+#      SAGE_LOCAL     -- prefix where packages are installed (usually $SAGE_ROOT/local)
+#      SAGE_INST_LOCAL-- prefix where to install this package;
+#                        this is set by the optional argument <installation tree>
+#                        and defaults to $SAGE_LOCAL.
 #      SAGE_DISTFILES -- directory that stores upstream tarballs
 #      SAGE_DESTDIR   -- temporary root the package will be installed to
 #      PKG_BASE       -- the base name of the package itself (e.g. 'patch')
@@ -112,8 +119,10 @@ cat >&2 <<MESSAGE
 $1
 ************************************************************************
 Please email sage-devel (http://groups.google.com/group/sage-devel)
-explaining the problem and including the log file
+explaining the problem and including the log files
   $SAGE_LOGS/$PKG_NAME.log
+and
+  $SAGE_ROOT/config.log
 Describe your computer, operating system, etc.
 MESSAGE
 
@@ -137,7 +146,8 @@ lookup_param()
 {
     local param=$1
     local file=$2
-    sed -n "s/^${param} *= *//p" $file
+    # Ignore errors if the file does not exist
+    sed -n "s/^${param} *= *//p" $file 2>/dev/null
 }
 
 write_to_tty()
@@ -184,14 +194,6 @@ if [ $? -ne 0 ]; then
     exit 1
 fi
 
-if [ -z "$SAGE_BUILD_DIR" ]; then
-    export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build"
-fi
-
-export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
-export SAGE_SPKG_SCRIPTS="$SAGE_LOCAL/var/lib/sage/scripts"
-export SAGE_SPKG_WHEELS="$SAGE_LOCAL/var/lib/sage/wheels"
-
 # Remove '.' from PYTHONPATH, to avoid trouble with setuptools / easy_install
 # (cf. #10192, #10176):
 if [ -n "$PYTHONPATH" ]; then
@@ -271,6 +273,28 @@ fi
 PKG_NAME="$PKG_SRC"
 PKG_BASE=`echo "$PKG_NAME" | sed 's/-.*//'` # strip version number
 
+case $# in
+    1)
+        SAGE_INST_LOCAL="$SAGE_LOCAL"
+        ;;
+    2)
+        SAGE_INST_LOCAL="$2"
+        ;;
+    *)
+        usage
+        exit 1
+        ;;
+esac
+export SAGE_INST_LOCAL
+
+if [ -z "$SAGE_BUILD_DIR" ]; then
+    export SAGE_BUILD_DIR="$SAGE_INST_LOCAL/var/tmp/sage/build"
+fi
+
+export SAGE_SPKG_INST="$SAGE_INST_LOCAL/var/lib/sage/installed"
+export SAGE_SPKG_SCRIPTS="$SAGE_INST_LOCAL/var/lib/sage/scripts"
+export SAGE_SPKG_WHEELS="$SAGE_INST_LOCAL/var/lib/sage/wheels"
+
 # USE_LOCAL_SCRIPTS is a flag that if non-empty will cause
 # this script to try to install the package using local metadata
 # i.e. use upstream tarballs (vs spkgs) and scripts located in build/pkgs/$PKG_BASE
@@ -294,7 +318,6 @@ fi
 USE_LOCAL_SCRIPTS=yes
 PKG_BASE_VER=`echo $PKG_VER | sed 's/\.p[0-9][0-9]*$//'`
 PKG_NAME_UPSTREAM=`lookup_param tarball "$PKG_SCRIPTS/checksums.ini" | sed "s/VERSION/$PKG_BASE_VER/"`
-echo "Found local metadata for $PKG_NAME"
 
 # Warning for experimental packages
 if [ x`cat "$PKG_SCRIPTS/type"` = x"experimental" -a $INFO = 0 ]; then
@@ -403,12 +426,12 @@ if [ ! -w "$SAGE_BUILD_DIR" ]; then
     error_msg "Error: no write access to build directory $SAGE_BUILD_DIR"
     exit 1
 fi
-if [ ! -d "$SAGE_LOCAL" ]; then
+if [ ! -d "$SAGE_INST_LOCAL" ]; then
     # If you just unpack Sage and run "sage -p <pkg>" then local does not yet exist
-    mkdir "$SAGE_LOCAL"
+    mkdir "$SAGE_INST_LOCAL"
 fi
-if [ ! -w "$SAGE_LOCAL" ]; then
-    error_msg "Error: no write access to installation directory $SAGE_LOCAL"
+if [ ! -w "$SAGE_INST_LOCAL" ]; then
+    error_msg "Error: no write access to installation directory $SAGE_INST_LOCAL"
     exit 1
 fi
 
@@ -502,7 +525,7 @@ 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"; do
+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
     source "\$lib"
     if [ \$? -ne 0 ]; then
         echo >&2 "Error: failed to source \$lib"
@@ -511,6 +534,8 @@ for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env-co
     fi
 done
 
+export SAGE_INST_LOCAL="$SAGE_INST_LOCAL"
+
 sdh_guard
 if [ \$? -ne 0 ]; then
     echo >&2 "Error: sdh_guard not found; Sage environment was not set up properly"
@@ -568,7 +593,7 @@ done
 if [ ! -f spkg-install ]; then
     echo '#!/usr/bin/env bash' > spkg-install
     if [ -x configure ]; then
-        echo './configure --prefix="$SAGE_LOCAL" && make && $SAGE_SUDO make install' >> spkg-install
+        echo './configure --prefix="$SAGE_INST_LOCAL" && make && $SAGE_SUDO make install' >> spkg-install
     elif [ -f setup.py ]; then
         echo 'python setup.py install' >> spkg-install
     else
@@ -609,6 +634,7 @@ export rsync_proxy=$http_proxy
 ##################################################################
 
 if [ "$UNAME" = "CYGWIN" ]; then
+    # This is a global lock - so we use SAGE_LOCAL, not SAGE_INST_LOCAL.
     if [ ! -d "$SAGE_LOCAL/var/lock" ]; then
         mkdir -p "$SAGE_LOCAL/var/lock"
     fi
@@ -627,9 +653,9 @@ export SAGE_DESTDIR="${SAGE_BUILD_DIR}/${PKG_NAME}/inst"
 
 # The actual prefix where the installation will be staged. This is the
 # directory that you need to work in if you want to change the staged
-# installation tree (before final installation to $SAGE_LOCAL) at the
+# installation tree (before final installation to $SAGE_INST_LOCAL) at the
 # end of spkg-install.
-export SAGE_DESTDIR_LOCAL="${SAGE_DESTDIR}${SAGE_LOCAL}"
+export SAGE_DESTDIR_LOCAL="${SAGE_DESTDIR}${SAGE_INST_LOCAL}"
 
 # First uninstall the previous version of this package, if any
 if [ "$KEEP_EXISTING" != "yes" ]; then

build/bin/sage-spkg-info

@@ -15,12 +15,27 @@ for ext in rst txt; do
 done
 if [ -r "$PKG_SCRIPTS/type" ] ; then
     echo
-    echo "== Type =="
+    echo "Type"
+    echo "----"
     echo
     cat "$PKG_SCRIPTS/type"
     echo
 fi
-echo "== Equivalent System Packages =="
+echo
+echo "Version Information"
+echo "-------------------"
+echo
+for a in package-version.txt requirements.txt install-requires.txt; do
+    if [ -f "$PKG_SCRIPTS"/"$a" ]; then
+        echo "$a::"
+        echo
+        sed 's/^/    /' "$PKG_SCRIPTS/$a"
+        echo
+    fi
+done
+echo
+echo "Equivalent System Packages"
+echo "--------------------------"
 echo
 PKG_DISTROS="$PKG_SCRIPTS"/distros
 for system_package_file in "$PKG_DISTROS"/*.txt; do
@@ -40,8 +55,15 @@ for system_package_file in "$PKG_DISTROS"/*.txt; do
                 echo "$system:"
                 ;;
         esac
-        printf "  "
-        sage-print-system-package-command $system --prompt --sudo install $system_packages
+        if [ -n "$OUTPUT_RST" ]; then
+            echo
+            echo ".. CODE-BLOCK:: bash"
+            echo
+        fi
+        sage-print-system-package-command $system --prompt='    $ ' --sudo install $system_packages
+        if [ -n "$OUTPUT_RST" ]; then
+            echo
+        fi
     fi
 done
 if [ -z "$system" ]; then
@@ -52,8 +74,13 @@ else
         echo "If the system package is installed, ./configure will check whether it can be used."
     else
         echo "However, these system packages will not be used for building Sage"
-        echo "because spkg-configure.m4 has not been written for this package;"
-        echo "see https://trac.sagemath.org/ticket/27330"
+        if [ -f "$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"
+        else
+            echo "because spkg-configure.m4 has not been written for this package;"
+            echo "see https://trac.sagemath.org/ticket/27330"
+        fi
     fi
 fi
 echo

build/make/Makefile.in

@@ -17,16 +17,18 @@
 # Always use bash for make rules
 SHELL = @SHELL@
 
-ifndef SAGE_SPKG_INST
-ifndef DEBUG_RULES
+# Check a variable that is only set in build/make/install, but not in sage-env, for example
+ifndef SAGE_PKGCONFIG
+# Set by build/bin/sage-sdist, which invokes the Makefile directly in
+# order to download upstream packages for distribution.
+ifndef SAGE_SPKG_COPY_UPSTREAM
 $(error This Makefile needs to be invoked by build/make/install)
-else
-# A dummy value for this variable for debugging purposes
-SAGE_SPKG_INST=installed
 endif
 endif
 
 # Directory to keep track of which packages are installed
+SAGE_SPKG_INST = $(SAGE_LOCAL)/var/lib/sage/installed
+
 INST = $(SAGE_SPKG_INST)
 
 # Aliases for mutually exclusive standard packages selected at configure time
@@ -588,6 +590,8 @@ $(1)-no-deps:
 		. '$$(SAGE_ROOT)/src/bin/sage-env' && \
 		. '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		. '$$(SAGE_ROOT)/build/bin/sage-build-env' && \
+		SAGE_SPKG_WHEELS=$$(SAGE_LOCAL)/var/lib/sage/wheels \
+		SAGE_INST_LOCAL=$$(SAGE_LOCAL) \
 		sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log'
 	touch "$$(INST)/$(1)-$(2)"
 

build/make/install

@@ -18,12 +18,6 @@ fi
 export SAGE_SHARE="$SAGE_LOCAL/share"
 export SAGE_PKGCONFIG="$SAGE_LOCAL/lib/pkgconfig"
 export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
-export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
-# Following line is duplicated here from build/bin/sage-spkg.
-# because the setting is also needed by some script packages.
-# The line here will be removed in #29386 (install script packages
-# via sage-spkg).
-export SAGE_SPKG_WHEELS="$SAGE_LOCAL/var/lib/sage/wheels"
 
 if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
     SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH