Merge tag '9.5.rc3' into public/scalar_elliptic_curve_endomorphisms

SageMath version 9.5.rc3, Release Date: 2022-01-18

.homebrew-build-env

@@ -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 polymake; do
+for l in readline bzip2 ntl polymake libpng bdw-gc primesieve; 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.rc0", 
-    "version": "9.5.rc0", 
+    "title": "sagemath/sage: 9.5.rc3", 
+    "version": "9.5.rc3", 
     "upload_type": "software", 
-    "publication_date": "2022-01-09", 
+    "publication_date": "2022-01-18", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,13 +15,13 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.rc0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.rc3", 
             "relation": "isSupplementTo"
         }, 
         {
             "scheme": "doi", 
             "identifier": "10.5281/zenodo.593563", 
-            "relation": "isVersionOf"
+            "relation": "isNewVersionOf"
         }
     ]
 }

.zenodo.json.in

@@ -21,7 +21,7 @@
         {
             "scheme": "doi", 
             "identifier": "10.5281/zenodo.593563", 
-            "relation": "isVersionOf"
+            "relation": "isNewVersionOf"
         }
     ]
 }

CITATION.cff

@@ -0,0 +1,11 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: SageMath
+abstract: SageMath is a free open-source mathematics software system.
+authors:
+- name: "The SageMath Developers"
+version: 9.5
+doi: 10.5281/zenodo.593563
+date-released: 2022-01-18
+repository-code: "https://github.com/sagemath/sage"
+url: "https://www.sagemath.org/"

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.rc0, Release Date: 2022-01-09
+SageMath version 9.5.rc3, Release Date: 2022-01-18

build/bin/sage-bootstrap-python

@@ -30,6 +30,9 @@ fi
 # is accessible by this python; this is to guard on Cygwin against Pythons
 # installed somewhere else in Windows.
 
+# Trac #29285: Do not accept pythons that manipulate PATH, such as
+# the shims provided by pyenv.
+
 # Trac #30008: Make it work even if the environment tries to sabotage UTF-8
 # operation in Python 3.0.x-3.6.x by setting LC_ALL=C or similar.
 
@@ -47,7 +50,7 @@ PYTHONS="python python3 python3.10 python3.9 python3.8 python3.7 python2.7 pytho
 for PY in $PYTHONS; do
     PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
     if [ -n "$PYTHON" ]; then
-        if "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from ssl import HAS_SNI; assert HAS_SNI; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
+        if CHECK_PATH="$PATH" "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from ssl import HAS_SNI; assert HAS_SNI; from os import listdir, environ; listdir(\"$(pwd)\"); assert environ[\"PATH\"] == environ[\"CHECK_PATH\"];" 2>/dev/null; then
             exec "$PYTHON" "$@"
         fi
     fi
@@ -56,10 +59,10 @@ done
 for PY in $PYTHONS; do
     PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
     if [ -n "$PYTHON" ]; then
-        if "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
+        if CHECK_PATH="$PATH" "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from os import listdir, environ; listdir(\"$(pwd)\"); assert environ[\"PATH\"] == environ[\"CHECK_PATH\"];" 2>/dev/null; then
             exec "$PYTHON" "$@"
         fi
     fi
 done
-echo >&2 "$0: error: none of $PYTHONS is a suitable Python with urllib"
+echo >&2 "$0: error: none of $PYTHONS is a suitable Python"
 exit 1

build/bin/sage-pip-install

@@ -30,6 +30,11 @@ PIP=pip3
 # running pip. This is implemented in the Python script sage-flock
 LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
 
+# Trac #33155: Pythons installed using the python.org macOS installers
+# for Python < 3.10 identify macOS Big Sur and newer as "10.16", causing
+# pip to refuse to install wheels tagged macosx_11_0_x86_64
+export SYSTEM_VERSION_COMPAT=0
+
 # Finally actually do the installation (the "SHARED" tells pip2/3-lock
 # to apply a shared lock)
 sage-flock -s $LOCK $PYTHON -m pip install $pip_install_flags "$@"

build/make/Makefile.in

@@ -183,6 +183,13 @@ else
 AM_V_at =
 endif
 
+# Trac #33125: Handle make options -n, -t, -q
+ifeq ($(foreach flag, n t q, $(findstring $(flag),$(filter-out --%,$(MAKEFLAGS)))),)
+PLUS = +
+else
+PLUS =
+endif
+
 # List of targets that can be run using `sage -i` or `sage -f`
 # These should generally have an associated -clean target for `sage -f` to
 # work correctly
@@ -603,7 +610,7 @@ $$($(4))/$(SPKG_INST_RELDIR)/$(1)-$(2): $(3)
 $(1): $$($(4))/$(SPKG_INST_RELDIR)/$(1)-$(2)
 
 $(1)-$(4)-no-deps:
-	+@if [ -z '$$($(4))' ]; then \
+	$(PLUS)@if [ -z '$$($(4))' ]; then \
 	    echo "Error: The installation tree $(4) has been disabled" 2>&1; \
 	    echo "$$($(4)_DISABLED_MESSAGE)" 2>&1; \
 	    exit 1; \

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=90c6a61858cddd0d4e3b65b05d899c742356a82e
-md5=eddfeb607a50616c02ca39dbfaae91a5
-cksum=3731009361
+sha1=82db5472ac5d29950254ec45b1f448dbc4f8e9f0
+md5=92c171e5c495c2c2f601d49f89cdaa36
+cksum=3258581436

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-464e8c3d08cd20837a05fc6afa7386f89a309133
+ad7e1731c0dd97d79084a0c3baa0022ba4cfff69

build/pkgs/cryptominisat/spkg-install.in

@@ -3,3 +3,7 @@ cd src
 sdh_cmake -DUSE_GAUSS='ON' $EXTRA_OPTS
 sdh_make VERBOSE=ON
 sdh_make_install VERBOSE=ON
+
+cd pycryptosat
+
+sdh_pip_install .

build/pkgs/iml/checksums.ini

@@ -1,4 +1,5 @@
 tarball=iml-VERSION.tar.bz2
-sha1=72355b1f4c4df8cd3ecf5fcbcbd72c9ad9afdba7
-md5=362f1a6a1d2df0c5f0ab41e5d2c87ac7
-cksum=507867168
+sha1=8aba468a62e6fb0584be9b014350b734663c0670
+md5=a8083e70c0c4378f69eb772c1eeed6f0
+cksum=2793221462
+upstream_url=https://trac.sagemath.org/raw-attachment/ticket/33195/iml-1.0.4p2.tar.bz2

build/pkgs/iml/package-version.txt

@@ -1 +1 @@
-1.0.4p1.p2
+1.0.4p2.p2

build/pkgs/iml/spkg-src

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 VERSION="1.0.4"
-PATCHLEVEL="p1"
+PATCHLEVEL="p2"
 
 if [ $# -ne 0 ]; then
     UPSTREAM_SOURCE_DIRECTORY=$1
@@ -22,4 +22,6 @@ else
 fi
 
 mv "iml-$VERSION" "iml-$VERSION$PATCHLEVEL"
+# Regenerate build scripts
+(cd "iml-$VERSION$PATCHLEVEL" && autoreconf -fi)
 tar cjf "iml-$VERSION$PATCHLEVEL.tar.bz2" "iml-$VERSION$PATCHLEVEL"

build/pkgs/numpy/spkg-install.in

@@ -1,3 +1,4 @@
+# -*- shell-script -*-
 cd src
 
 set -e
@@ -39,6 +40,7 @@ fi
 
 ################################################
 
-eval sdh_pip_install \
+# Trac #33138: numpy is a PEP 517 package, so the crucial "--build-option"s would be ignored.
+eval sdh_pip_install --no-use-pep517 \
      $(eval sdh_prefix_args "--build-option" build ${NUMPY_CONFIG} ${NUMPY_FCONFIG}) \
      .

build/pkgs/ore_algebra/requirements.txt

@@ -1 +1 @@
-git+https://github.com/mkauers/ore_algebra@6826ac49b4cdf66a563449aced21a2fd1fd085c9#egg=ore_algebra
+git+https://github.com/mkauers/ore_algebra@cfcb386f2cc1d3e044c71dfb149444355b16d775#egg=ore_algebra

build/pkgs/pyzmq/spkg-install.in

@@ -1,10 +1,3 @@
 cd src
-
-# Generate setup.cfg
-cat > setup.cfg <<EOF
-[global]
-no_libzmq_extension = True
-EOF
-
 # Configure and install
 sdh_pip_install .

build/pkgs/qhull/spkg-configure.m4

@@ -19,8 +19,11 @@ SAGE_SPKG_CONFIGURE([qhull], [
                ], [
                   AC_MSG_RESULT([no. Install qhull])
                   sage_spkg_install_qhull=yes
-               ]) dnl CHECK_HEADER
-     ]) dnl COMPARE_VERSION
+               ]), dnl CHECK_HEADER
+           ], [
+               AC_MSG_RESULT([no. Install qhull])
+               sage_spkg_install_qhull=yes
+           ]) dnl AX_COMPARE_VERSION
     ]) dnl IF
     m4_popdef([SAGE_QHULL_MINVER])
 ])

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.5.rc0
+9.5.rc3

src/VERSION.txt

@@ -1 +1 @@
-9.5.rc0
+9.5.rc3

src/bin/sage-version.sh

@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='9.5.rc0'
-SAGE_RELEASE_DATE='2022-01-09'
-SAGE_VERSION_BANNER='SageMath version 9.5.rc0, Release Date: 2022-01-09'
+SAGE_VERSION='9.5.rc3'
+SAGE_RELEASE_DATE='2022-01-18'
+SAGE_VERSION_BANNER='SageMath version 9.5.rc3, Release Date: 2022-01-18'

src/doc/en/installation/launching.rst

@@ -125,14 +125,20 @@ convenience, it is possible to link your installation of SageMath into
 your Jupyter installation, adding it to the list of available kernels
 that can be selected in the notebook or JupyterLab interface.
 
-If ``$SAGE_LOCAL`` is the installation prefix of your Sage
-installation (the default is ``$SAGE_ROOT/local``) and you can start
-the Jupyter notebook by typing ``jupyter notebook``, then the
-following command will install SageMath as a new kernel.
+Assuming that SageMath can be invoked by typing ``sage``, you can use
 
 .. CODE-BLOCK:: bash
 
-    jupyter kernelspec install --user $SAGE_LOCAL/share/jupyter/kernels/sagemath
+    sage -sh -c 'ls -d $SAGE_VENV/share/jupyter/kernels/sagemath'
+
+to find the location of the SageMath kernel description.
+
+Assuming that the Jupyter notebook can be started by typing ``jupyter notebook``,
+the following command will install SageMath as a new kernel.
+
+.. CODE-BLOCK:: bash
+
+    jupyter kernelspec install --user $(sage -sh -c 'ls -d $SAGE_VENV/share/jupyter/kernels/sagemath')
 
 This installs the kernel under the name ``sagemath``.  If you wish to
 rename it to something more specific in order to distinguish between
@@ -141,32 +147,35 @@ different installations of SageMath, you can use the additional option
 
 .. CODE-BLOCK:: bash
 
-    jupyter kernelspec install --user $SAGE_LOCAL/share/jupyter/kernels/sagemath --name sagemath-dev-worktree
+    jupyter kernelspec install --user $(sage -sh -c 'ls -d $SAGE_VENV/share/jupyter/kernels/sagemath') --name sagemath-dev-worktree
 
 The ``jupyter kernelspec`` approach by default does lead to about 2Gb of
-sagemath documentation being copied into your personal jupyter configuration
+SageMath documentation being copied into your personal jupyter configuration
 directory. You can avoid that by instead putting a symlink in the relevant spot.
-Assuming that sagemath is properly installed, you can use
+and
 
 .. CODE-BLOCK:: bash
 
-    sage -sh -c 'ls -d $SAGE_LOCAL/share/jupyter/kernels/sagemath'
+    jupyter --paths
 
-to find location of the sagemath kernel description and
+to find valid data directories for your Jupyter installation.
+A command along the lines of
 
 .. CODE-BLOCK:: bash
 
-    jupyter --paths
+    ln -s $(sage -sh -c 'ls -d $SAGE_VENV/share/jupyter/kernels/sagemath') $HOME/.local/share/jupyter
 
-to find valid data directories for your jupyter installation.
-A command along the lines of
+can then be used to create a symlink to the SageMath kernel description
+in a location where your own ``jupyter`` can find it.
+
+If you have installed SageMath from source, the alternative command
 
 .. CODE-BLOCK:: bash
 
-    ln -s `sage -sh -c 'ls -d $SAGE_LOCAL/share/jupyter/kernels/sagemath'` $HOME/.local/share/jupyter
+    ln -s $(sage -sh -c 'ls -d $SAGE_ROOT/venv/share/jupyter/kernels/sagemath') $HOME/.local/share/jupyter
 
-can then be used to create a symlink to the sagemath kernel description
-in a location where your own ``jupyter`` can find it.
+creates a symlink that will stay current even if you switch to a different Python version
+later.
 
 To get the full functionality of the SageMath kernel in your global
 Jupyter installation, the following Notebook Extension packages also

src/sage/all.py

@@ -96,6 +96,10 @@
 warnings.filterwarnings('ignore', category=DeprecationWarning,
                         module='pythran')
 
+warnings.filterwarnings('ignore', category=DeprecationWarning,
+                        message='The distutils(.sysconfig module| package) is deprecated',
+                        module='Cython|distutils|numpy|sage.env|sage.features')
+
 ################ end setup warnings ###############################
 
 

src/sage/libs/linbox/fflas.pxd

@@ -1,4 +1,12 @@
-# distutils: extra_compile_args = FFLASFFPACK_CFLAGS
+# Trac #33153: fflas-ffpack-2.4.3 is missing a return value in one of
+# its functions and runs afoul of -Werror=return-type. Compounding the
+# problem on openSUSE tumbleweed, the CFLAGS in python's sysconfig
+# contain -Werror=return-type and wind up being used to compile this
+# extension. To avoid a compilation failure on that platform, we
+# temporarily append "-Wno-error=return-type" to those flags.
+#
+# distutils: extra_compile_args = FFLASFFPACK_CFLAGS -Wno-error=return-type
+#
 # distutils: include_dirs = FFLASFFPACK_INCDIR
 # distutils: libraries = FFLASFFPACK_LIBRARIES
 # distutils: library_dirs = FFLASFFPACK_LIBDIR

src/sage/rings/integer.pyx

@@ -7240,10 +7240,30 @@ cdef int sizeof_Integer
 
 # We use a global Integer element to steal all the references
 # from. DO NOT INITIALIZE IT AGAIN and DO NOT REFERENCE IT!
-#
-# Use actual calculation to avoid libgmp's new lazy allocation :trac:`31340`
 cdef Integer global_dummy_Integer
-global_dummy_Integer = Integer(1) - Integer(1)
+global_dummy_Integer = Integer()
+# Reallocate to one limb to fix :trac:`31340` and :trac:`33081`
+_mpz_realloc(global_dummy_Integer.value, 1)
+
+def _check_global_dummy_Integer():
+    """
+    Return true if the global dummy Integer is ok.
+
+    TEST::
+
+        sage: from sage.rings.integer import _check_global_dummy_Integer
+        sage: _check_global_dummy_Integer()
+        True
+    """
+    # Check that it has exactly one limb allocated
+    # This is assumed later in fast_tp_new() :trac:`33081`
+    cdef mpz_ptr dummy = global_dummy_Integer.value
+    if dummy._mp_alloc == 1 and dummy._mp_size == 0:
+        return True
+
+    raise AssertionError(
+      "global dummy Integer is corrupt (_mp_alloc = %d, _mp_size = %d)"
+      % (dummy._mp_alloc, dummy._mp_size))
 
 
 # A global pool for performance when integers are rapidly created and destroyed.
@@ -7318,6 +7338,8 @@ cdef PyObject* fast_tp_new(type t, args, kwds) except NULL:
         #  various internals described here may change in future GMP releases.
         #  Applications expecting to be compatible with future releases should use
         #  only the documented interfaces described in previous chapters."
+        #
+        # NOTE: This assumes global_dummy_Integer.value._mp_alloc == 1
         new_mpz = <mpz_ptr>((<Integer>new).value)
         new_mpz._mp_d = <mp_ptr>check_malloc(GMP_LIMB_BITS >> 3)
 

src/sage/version.py

@@ -1,5 +1,5 @@
 # Sage version information for Python scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-version = '9.5.rc0'
-date = '2022-01-09'
-banner = 'SageMath version 9.5.rc0, Release Date: 2022-01-09'
+version = '9.5.rc3'
+date = '2022-01-18'
+banner = 'SageMath version 9.5.rc3, Release Date: 2022-01-18'