Merge branch 'develop' into improve_approximate_order_on__getitem__calls

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta4", 
-    "version": "10.0.beta4", 
+    "title": "sagemath/sage: 10.0.beta5", 
+    "version": "10.0.beta5", 
     "upload_type": "software", 
-    "publication_date": "2023-03-12", 
+    "publication_date": "2023-03-19", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta4", 
+            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta5", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -80,42 +80,6 @@ download:
 dist: build/make/Makefile
 	./sage --sdist
 
-pypi-sdists: sage_setup
-	./sage --sh build/pkgs/sage_conf/spkg-src
-	./sage --sh build/pkgs/sage_sws2rst/spkg-src
-	./sage --sh build/pkgs/sage_docbuild/spkg-src
-	./sage --sh build/pkgs/sage_setup/spkg-src
-	./sage --sh build/pkgs/sagelib/spkg-src
-	./sage --sh build/pkgs/sagemath_objects/spkg-src
-	./sage --sh build/pkgs/sagemath_categories/spkg-src
-	./sage --sh build/pkgs/sagemath_environment/spkg-src
-	./sage --sh build/pkgs/sagemath_repl/spkg-src
-	@echo "Built sdists are in upstream/"
-
-# Ensuring wheels are present, even for packages that may have been installed
-# as editable. Until we have better uninstallation of script packages, we
-# just remove the timestamps, which will lead to rebuilds of the packages.
-PYPI_WHEEL_PACKAGES = sage_sws2rst sage_setup sagemath_environment sagemath_objects sagemath_repl sagemath_categories
-pypi-wheels:
-	for a in $(PYPI_WHEEL_PACKAGES); do \
-	    rm -f venv/var/lib/sage/installed/$$a-*; \
-	done
-	for a in $(PYPI_WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
-	done
-	@echo "Built wheels are in venv/var/lib/sage/wheels/"
-
-# sage_docbuild is here, not in PYPI_WHEEL_PACKAGES, because it depends on sagelib
-WHEEL_PACKAGES = $(PYPI_WHEEL_PACKAGES) sage_conf sagelib sage_docbuild
-wheels:
-	for a in $(WHEEL_PACKAGES); do \
-	    rm -f venv/var/lib/sage/installed/$$a-*; \
-	done
-	for a in $(WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
-	done
-	@echo "Built wheels are in venv/var/lib/sage/wheels/"
-
 ###############################################################################
 # Cleaning up
 ###############################################################################
@@ -380,7 +344,6 @@ list:
 	@$(MAKE) --silent -f build/make/Makefile SAGE_PKGCONFIG=dummy $@
 
 .PHONY: default build dist install micro_release \
-	pypi-sdists pypi-wheels wheels \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta4, Release Date: 2023-03-12
+SageMath version 10.0.beta5, Release Date: 2023-03-19

build/make/Makefile.in

@@ -128,7 +128,23 @@ PIP_PACKAGES = @SAGE_PIP_PACKAGES@
 # Packages that use the 'script' package build rules
 SCRIPT_PACKAGES = @SAGE_SCRIPT_PACKAGES@
 
-
+# Packages for which we build wheels for PyPI
+PYPI_WHEEL_PACKAGES =				\
+	sage_sws2rst				\
+	sage_setup				\
+	sagemath_environment			\
+	sagemath_objects			\
+	sagemath_repl				\
+	sagemath_categories
+
+# sage_docbuild is here, not in PYPI_WHEEL_PACKAGES, because it depends on sagelib
+WHEEL_PACKAGES = $(PYPI_WHEEL_PACKAGES)		\
+	sage_conf				\
+	sagelib					\
+	sage_docbuild
+
+# Packages for which build sdists for PyPI
+PYPI_SDIST_PACKAGES = $(WHEEL_PACKAGES)
 
 # Generate the actual inst_<pkgname> variables; for each package that is
 # actually built this generates a line like:
@@ -198,6 +214,7 @@ SAGE_I_TARGETS = sagelib doc
 # Tell make not to look for files with these names:
 .PHONY: all all-sage all-toolchain all-build all-sageruntime \
 	all-start build-start base toolchain toolchain-deps base-toolchain \
+	pypi-sdists pypi-wheels wheels \
 	sagelib \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
 	doc-uninstall \
@@ -418,6 +435,25 @@ list-broken-packages: auditwheel_or_delocate
 	    echo >&2 "$$fix_broken_packages"; \
 	fi
 
+pypi-sdists: $(PYPI_SDIST_PACKAGES:%=%-sdist)
+	@echo "Built sdists are in upstream/"
+
+# Ensuring wheels are present, even for packages that may have been installed
+# as editable. Until we have better uninstallation of script packages, we
+# just remove the timestamps, which will lead to rebuilds of the packages.
+pypi-wheels:
+	for a in $(PYPI_WHEEL_PACKAGES); do \
+	    rm -f $(SAGE_VENV)/var/lib/sage/installed/$$a-*; \
+	done
+	$(MAKE_REC) SAGE_EDITABLE=no SAGE_WHEELS=yes $(PYPI_WHEEL_PACKAGES)
+	@echo "Built wheels are in venv/var/lib/sage/wheels/"
+
+wheels:
+	for a in $(WHEEL_PACKAGES); do \
+	    rm -f $(SAGE_VENV)/var/lib/sage/installed/$$a-*; \
+	done
+	$(MAKE_REC) SAGE_EDITABLE=no SAGE_WHEELS=yes $(WHEEL_PACKAGES)
+	@echo "Built wheels are in venv/var/lib/sage/wheels/"
 
 #==============================================================================
 # Setting SAGE_CHECK... variables
@@ -711,6 +747,13 @@ $(1)-uninstall: $(1)-$(4)-uninstall
 
 $(1)-clean: $(1)-uninstall
 
+$(1)-sdist: FORCE python_build sage_setup cython
+	$(AM_V_at) cd '$$(SAGE_ROOT)' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-src-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-src'
+
 # Recursive tox invocation (note - we do not set the environment here).
 # Setting SAGE_SPKG_WHEELS is for the benefit of sagelib's tox.ini
 $(1)-tox-%: FORCE

build/pkgs/_prereq/distros/fedora.txt

@@ -30,7 +30,6 @@ gcc-c++
 # The need for which comes [...] from MPIR's configure script
 findutils
 which
-# Needed for pcre configure, see https://github.com/sagemath/sage/issues/29129:
 diffutils
 # Needed for openssl 3.0
 perl-IPC-Cmd

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=d8ef4b8b0d227b2530cff20c65911eb9587828a3
-md5=f58322981d5c5e26b1d9eadf3c2a9132
-cksum=3821522607
+sha1=0ea92e19072c843aa21527e051eff0a0f97eb9ad
+md5=44e659f4d263acad8194e16952762a82
+cksum=3343113057

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-d6c38e59d84f0dcb7c08110445050c1c370f7440
+49c2cd323e638cdfb0444d72daad21b4ddbd1887

build/pkgs/gap/checksums.ini

@@ -1,5 +1,5 @@
 tarball=gap-VERSION.tar.gz
-sha1=4ecdd281b8f430282fb9b12690b06e0a26abde10
-md5=85dc9e459d5b6c66fcad9f468afd3e3e
-cksum=1351843158
+sha1=a6e36f3f874a2c46f51561402634497eab705cca
+md5=c5cd9f272f2703d7a3649ad7193b2d90
+cksum=2760477284
 upstream_url=https://github.com/gap-system/gap/releases/download/vVERSION/gap-VERSION.tar.gz

build/pkgs/gap/package-version.txt

@@ -1 +1 @@
-4.11.1
+4.12.2

build/pkgs/gap/patches/atlasrep-dont_use_network_by_default.patch

@@ -0,0 +1,11 @@
+--- a/pkg/atlasrep/gap/userpref.g	2022-09-06 17:41:17.000000000 -0300
++++ b/pkg/atlasrep/gap/userpref.g	2022-10-29 07:46:48.580833277 -0300
+@@ -46,7 +46,7 @@
+ this information depends on the value of the preference at the time \
+ when the AtlasRep package and its data extensions get loaded."
+     ],
+-  default:= true,
++  default:= false,
+   values:= [ true, false ],
+   multi:= false,
+   package:= "AtlasRep",

build/pkgs/gap/spkg-check.in

@@ -3,6 +3,13 @@ cd src
 # #28728: Fix test failure in tst/testinstall/strings.tst
 export LC_CTYPE=en_US.UTF-8
 
+# #34391: in GAP 4.12 some packages need GAP package io
+#         to let tests run, otherwise this hangs. Thus we install io here.
+cd pkg/io
+./configure --with-gaproot=../..
+make
+cd ../..
+
 make testinstall
 if [[ $? -ne 0 ]]; then
     exit 1

build/pkgs/gap/spkg-install.in

@@ -8,46 +8,25 @@ export CFLAGS=$CFLAGS_NON_NATIVE
 export CXXFLAGS=$CXXFLAGS_NON_NATIVE
 
 GAP_BUILD_ROOT="$(pwd)"
-GAP_ROOT="$SAGE_LOCAL/share/gap"
-DESTDIR_GAP_ROOT="$SAGE_DESTDIR$GAP_ROOT"
+GAP_ROOT="$SAGE_LOCAL/lib/gap"
 
 # Enable debug info if requested.
 # Note that -g3 allows you to use preprocessor macros in gdb which are widely used
 if [ "$SAGE_DEBUG" = yes ] ; then
     export CFLAGS="-O0 -g3 -DDEBUG_MASTERPOINTERS -DDEBUG_GLOBAL_BAGS -DDEBUG_FUNCTIONS_BAGS $CFLAGS"
 fi
 
-sdh_configure $SAGE_CONFIGURE_GMP
-sdh_make -j1
+# LDFLAGS hack below needed by Semigroups package
+sdh_configure $SAGE_CONFIGURE_GMP LDFLAGS="-pthread" --prefix=$SAGE_LOCAL
+sdh_make
 
-# GAP's "make install" is work in progress; we use bits and pieces of it
-# but we install many things manually.
-sdh_make install-headers install-libgap
-
-# Install config.h, which is not currently handled by `make install-headers`
-sdh_install gen/config.h "$SAGE_LOCAL/include/gap"
-
-# Now install the gap executable as "gap-bin"; it will be called normally
-# through our wrapper script that sets the appropriate GAP_ROOT
-SAGE_BIN="$SAGE_LOCAL/bin"
-mkdir -p "$SAGE_DESTDIR$SAGE_BIN" || sdh_die "Failed to create the directory $SAGE_BIN"
-
-./libtool --mode=install install gap "$SAGE_DESTDIR$SAGE_BIN/gap-bin" || \
-    sdh_die "Failed to install gap-bin to $SAGE_BIN"
-
-./libtool --mode=install install gac "$SAGE_DESTDIR$SAGE_BIN/gac" || \
-    sdh_die "Failed to install gac to $SAGE_BIN"
-
-# Now copy additional files GAP needs to run (and a few optional bits) into
-# GAP_ROOT; we don't need everything from the source tree
-sdh_install bin doc gen grp lib src tst sysinfo.gap "$GAP_ROOT"
-
-# GAP's copy of libtool is also used by the toolchain for build GAP packages
-# (i.e. by gac)
-sdh_install libtool "$GAP_ROOT"
+sdh_make_install
+# sdh_make install-headers install-libgap
+# The 'packagemanager' package expects this https://github.com/gap-packages/PackageManager/issues/105
+mkdir -p "$SAGE_LOCAL/lib/gap/bin"
 
 # Install only the minimal packages GAP needs to run
-sdh_install pkg/GAPDoc-* pkg/primgrp-* pkg/SmallGrp-* pkg/transgrp "$GAP_ROOT"/pkg
+sdh_install pkg/gapdoc pkg/primgrp pkg/smallgrp pkg/transgrp "$GAP_ROOT"/pkg
 
 # Install additional packages that are not strictly required, but that are
 # typically "expected" to be loaded: These are the default packages that are
@@ -58,50 +37,25 @@ sdh_install pkg/GAPDoc-* pkg/primgrp-* pkg/SmallGrp-* pkg/transgrp "$GAP_ROOT"/p
 # Also include atlasrep which is a dependency of tomlib
 sdh_install \
     pkg/atlasrep \
-    pkg/autpgrp-* \
-    pkg/alnuth-* \
-    pkg/crisp-* \
-    pkg/ctbllib-* \
-    pkg/FactInt-* \
+    pkg/autodoc \
+    pkg/autpgrp \
+    pkg/alnuth \
+    pkg/crisp \
+    pkg/ctbllib \
+    pkg/factint \
     pkg/fga \
-    pkg/irredsol-* \
-    pkg/laguna-* \
-    pkg/PackageManager-* \
-    pkg/polenta-* \
-    pkg/polycyclic-* \
-    pkg/resclasses-* \
-    pkg/sophus-* \
-    pkg/tomlib-* \
+    pkg/irredsol \
+    pkg/laguna \
+    pkg/packagemanager \
+    pkg/polenta \
+    pkg/polycyclic \
+    pkg/radiroot \
+    pkg/resclasses \
+    pkg/sophus \
+    pkg/tomlib \
+    pkg/utils \
     "$GAP_ROOT"/pkg
 
-# Install the GAP startup script; ensure it is executable
-sdh_install -T ../gap "$SAGE_BIN/gap"
-chmod +x "$SAGE_DESTDIR$SAGE_BIN/gap"
-
-# Create symlinks under $GAP_ROOT for these executables, as they are expected
-# (especially when building kernel packages) to exist
-ln -sf "../../bin/gap-bin" "$DESTDIR_GAP_ROOT/gap"
-ln -sf "../../bin/gac" "$DESTDIR_GAP_ROOT/gac"
-
-# Fix the $GAP_ROOT/bin/<arch>/src symlink to be relative (otherwise it links
-# to the actual path of the sources GAP was compiled from)
-for srclink in "$DESTDIR_GAP_ROOT"/bin/*/src; do
-    rm -f "$srclink"
-    ln -s "../../src" "$srclink"
-done
-
-# Additional fixups for some files after they have been copied into their
-# destination directory.  gac and sysinfo.gap are generated files that contain
-# in them hard-coded references to the GAP build directory, which will soon
-# 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://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" || \
-    sdh_die "Failed to fix up hard-coded paths in GAP build tools."
-
 # TODO: This seems unnecessary--we are already installing all of doc/ to
 # GAP_ROOT, which is necessary for some functionality in GAP to work.  Do
 # we need this?  Maybe doc/gap could just be a symlink to gap/doc??

build/pkgs/gap/spkg-legacy-uninstall

@@ -4,6 +4,8 @@ rm -rf "$SAGE_LOCAL/gap/gap-4."*
 rm -rf "$SAGE_SHARE/gap"
 rm -f "$SAGE_LOCAL/gap/latest"
 rm -f "$SAGE_LOCAL/bin/gap"
+rm -f "$SAGE_LOCAL/bin/gac"
 
-# Remove old libgap headers
+# Remove old libgap headers and library
 rm -rf "$SAGE_LOCAL/include/gap"
+rm -rf "$SAGE_LOCAL/lib/gap"