Merge tag '9.3.rc3' into t/27366/affine-hull-more

SageMath version 9.3.rc3, Release Date: 2021-04-12

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.rc2", 
-    "version": "9.3.rc2", 
+    "title": "sagemath/sage: 9.3.rc3", 
+    "version": "9.3.rc3", 
     "upload_type": "software", 
-    "publication_date": "2021-04-06", 
+    "publication_date": "2021-04-12", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc2", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc3", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.rc2, Release Date: 2021-04-06
+SageMath version 9.3.rc3, Release Date: 2021-04-12

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=08f282239756f779e6b97cf391fbd0e22d6129a9
-md5=49062bca12e661eaa98631ae44e843bf
-cksum=1707016786
+sha1=8e87b8d927704c25058ba2d9595e48e22062197f
+md5=ebdea78d9fb120ab8e31f4ea5dd01d8e
+cksum=3284139585

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-4275b275a2cb292826cdeb078765331dcda54c96
+c0dc957ff06d230f943cad6ae12dc3b028eec49c

build/pkgs/lrslib/distros/debian.txt

@@ -0,0 +1 @@
+lrslib

build/pkgs/lrslib/distros/fedora.txt

@@ -0,0 +1 @@
+lrslib

build/pkgs/lrslib/distros/freebsd.txt

@@ -0,0 +1 @@
+math/lrslib

build/pkgs/lrslib/distros/gentoo.txt

@@ -0,0 +1 @@
+sci-libs/lrslib

build/pkgs/lrslib/distros/nix.txt

@@ -0,0 +1 @@
+lrs

build/pkgs/lrslib/spkg-configure.m4

@@ -0,0 +1,7 @@
+SAGE_SPKG_CONFIGURE([lrslib], [
+    dnl System lrslib may already be 7.x, which may be compiled with FLINT
+    SAGE_SPKG_DEPCHECK([gmp mpir flint], [
+        AC_CHECK_PROGS([LRSNASH], [lrsnash])
+        AS_IF([test -z "$LRSNASH"], [sage_spkg_install_lrslib=yes])
+    ])
+])

build/pkgs/pynac/package-version.txt

@@ -1 +1 @@
-0.7.27.p3
+0.7.27.p4

build/pkgs/pynac/patches/handle_factor.patch

@@ -0,0 +1,43 @@
+diff --git a/ginac/expairseq.cpp b/ginac/expairseq.cpp
+index dd87d18..556b713 100644
+--- a/ginac/expairseq.cpp
++++ b/ginac/expairseq.cpp
+@@ -1032,7 +1032,12 @@ void expairseq::make_flat(const epvector &v, bool do_index_renaming)
+
+ 		if (ex_to<basic>(elem.rest).tinfo()==this->tinfo() &&
+ 		    this->can_make_flat(elem)) {
+-			ex newrest = mf.handle_factor(elem.rest, elem.coeff);
++		        ex newrest;
++		        if (is_exactly_a<numeric>(elem.coeff) and elem.coeff.is_zero()) {
++		            newrest = default_overall_coeff();
++		        } else {
++		            newrest = elem.rest;
++		        }
+ 			const expairseq &subseqref = ex_to<expairseq>(newrest);
+ 			combine_overall_coeff(subseqref.overall_coeff,
+ 			                      ex_to<numeric>(elem.coeff));
+@@ -1043,15 +1048,15 @@ void expairseq::make_flat(const epvector &v, bool do_index_renaming)
+ 			if (elem.is_canonical_numeric())
+ 				combine_overall_coeff(ex_to<numeric>(mf.handle_factor(elem.rest, _ex1)));
+ 			else {
+-				const ex& rest = elem.rest;
+-				const ex& newrest = mf.handle_factor(rest, elem.coeff);
+-                                if (newrest.is_zero())
+-                                        combine_overall_coeff(*_num0_p);
+-				else if (are_ex_trivially_equal(newrest, rest))
+-					seq.push_back(elem);
+-				else
+-					seq.emplace_back(newrest, elem.coeff);
+-			}
++			        if ((is_exactly_a<numeric>(elem.coeff) and elem.coeff.is_zero())
++			                or (is_exactly_a<numeric>(elem.rest)
++			                    and (ex_to<numeric>(elem.rest).is_equal(default_overall_coeff())))) {
++			            combine_overall_coeff(default_overall_coeff());
++			        }
++			        else {
++			                seq.push_back(elem);
++			        }
++			    }
+ 		}
+ 	}
+ }

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.3.rc2
+9.3.rc3

build/pkgs/singular/checksums.ini

@@ -1,5 +1,5 @@
 tarball=singular-VERSION.tar.gz
-sha1=3c8e4d867a050d676f1eaee622694d30c1e00bcc
-md5=edd42d42f3ddaa4f495a2111c72bf0da
-cksum=1198605855
-upstream_url=https://trac.sagemath.org/raw-attachment/ticket/31552/singular-VERSION.tar.gz
+sha1=dc0f618a669fb8c5e56166d82edc494a4e5504be
+md5=2354d9456c9fad0353b3157aff82796f
+cksum=2872654555
+upstream_url=https://github.com/mkoeppe/Singular/releases/download/singular-VERSION/singular-VERSION.tar.gz

build/pkgs/singular/package-version.txt

@@ -1 +1 @@
-4.2.0p1+2021-03-24+sage-2
+4.2.0p1+2021-04-06+sage

build/pkgs/symengine/checksums.ini

@@ -1,5 +1,5 @@
 tarball=symengine-VERSION.tar.gz
-sha1=abd7d39b1b724f47bcdc5b1d811cf33f2c413aea
-md5=3c0df2b14310467c6d45bc26a557324b
-cksum=100973134
+sha1=a4d30b3c417c3939383384b95c8b3c248e4e413e
+md5=72b8f1442fd3084c96e59d9fe87eec1a
+cksum=3356860163
 upstream_url=https://github.com/symengine/symengine/releases/download/vVERSION/symengine-VERSION.tar.gz

build/pkgs/symengine/package-version.txt

@@ -1 +1 @@
-0.6.0
+0.7.0

build/pkgs/symengine/patches/1749.patch

@@ -0,0 +1,44 @@
+From 713c096527291b24a8bee47895859f202b6eaa92 Mon Sep 17 00:00:00 2001
+From: Isuru Fernando <[email protected]>
+Date: Sat, 20 Mar 2021 13:33:17 -0500
+Subject: [PATCH] Check for flint-arb
+
+---
+ cmake/FindARB.cmake       | 2 +-
+ cmake/LibFindMacros.cmake | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/cmake/FindARB.cmake b/cmake/FindARB.cmake
+index 770da3133..281c5beae 100644
+--- a/cmake/FindARB.cmake
++++ b/cmake/FindARB.cmake
+@@ -1,7 +1,7 @@
+ include(LibFindMacros)
+
+ libfind_include(arb.h arb)
+-libfind_library(arb arb)
++libfind_library(arb arb flint-arb)
+
+ set(ARB_LIBRARIES ${ARB_LIBRARY})
+ set(ARB_INCLUDE_DIRS ${ARB_INCLUDE_DIR})
+diff --git a/cmake/LibFindMacros.cmake b/cmake/LibFindMacros.cmake
+index 68fcaa426..06aa3f5ba 100644
+--- a/cmake/LibFindMacros.cmake
++++ b/cmake/LibFindMacros.cmake
+@@ -28,7 +28,7 @@ function (libfind_library libname pkg)
+
+     find_library(${LIBNAME}_LIBRARY
+         NAMES
+-            ${libname}
++            ${libname} ${ARGN}
+     )
+
+     if (NOT TARGET ${libname})
+@@ -42,6 +42,6 @@ function (libfind_include HEADER pkg)
+
+     find_path(${PKG}_INCLUDE_DIR
+         NAMES
+-            ${HEADER}
++            ${HEADER} ${ARGN}
+     )
+ endfunction()

build/pkgs/symengine_py/checksums.ini

@@ -1,5 +1,5 @@
 tarball=symengine.py-VERSION.tar.gz
-sha1=40df2b8f406b6ac4a86c83a82d31593b5738a470
-md5=52b035da7851414d74f3bde83b6c2976
-cksum=2829876300
+sha1=8535fea222d85c5afefc5122dd5d43d91aa4ebb0
+md5=0167a0081410be856edc8ee245005576
+cksum=4011943203
 upstream_url=https://github.com/symengine/symengine.py/archive/vVERSION.tar.gz

build/pkgs/symengine_py/package-version.txt

@@ -1 +1 @@
-0.6.1
+0.7.0.post2

build/pkgs/sympy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=sympy-VERSION.tar.gz
-sha1=a96e0827a8fd7325b4f0099bb92ba89ae88bace4
-md5=58764f19e5d8ee1acec6264456191699
-cksum=4154398619
+sha1=e9a321af141998638cc822505f07107736776c39
+md5=f5973bcbe33fdc86203ca397cc901994
+cksum=1357232010
 upstream_url=https://github.com/sympy/sympy/releases/download/sympy-VERSION/sympy-VERSION.tar.gz

build/pkgs/sympy/package-version.txt

@@ -1 +1 @@
-1.7
+1.7.1

configure.ac

@@ -101,6 +101,11 @@ AC_ARG_ENABLE([debug],
 
 AC_ARG_VAR(SAGE_DEBUG, controls debugging support: "no" debugging; debugging "symbols" (default); build debug version ("yes"))
 
+AC_ARG_ENABLE([editable],
+              [AS_HELP_STRING([--enable-editable],
+                              [use an editable install of the Sage library])],
+              [AC_SUBST([SAGE_EDITABLE], [yes])])
+
 # Check whether we are on a supported platform
 AC_CANONICAL_BUILD()
 AC_CANONICAL_HOST()

src/VERSION.txt

@@ -1 +1 @@
-9.3.rc2
+9.3.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='9.3.rc2'
-SAGE_RELEASE_DATE='2021-04-06'
-SAGE_VERSION_BANNER='SageMath version 9.3.rc2, Release Date: 2021-04-06'
+SAGE_VERSION='9.3.rc3'
+SAGE_RELEASE_DATE='2021-04-12'
+SAGE_VERSION_BANNER='SageMath version 9.3.rc3, Release Date: 2021-04-12'

src/doc/en/installation/binary.rst

@@ -87,24 +87,27 @@ installation.
 macOS
 -----
 
-On macOS there are three possible binaries for each version. They can
-be recognized by their suffixes:
+On macOS there are two possible binaries for each version. They can be
+recognized by their suffixes, but their actual contents are identical.
 
 - ``tar.bz2``: a binary tarball
 - ``dmg``: a compressed image of the binary
-- ``app.dmg``: a compressed image of a full macOS application (with
-  shortcuts)
 
-This section explains how to install from ``dmg`` or ``app.dmg``. For
-the installation of the binary tarball ``tar.bz2`` just follow the steps
+This section explains how to install from ``dmg``. For the
+installation of the binary tarball ``tar.bz2`` just follow the steps
 of the Linux installation.
 
-After downloading the file, double click on the dmg file to mount it which will
-take some time.  Then drag the folder ``SageMath`` that just appeared to
-``/Applications/``. If you did download the app, an icon should have appeared
-on your desktop. Simply use it. In both situations you might want to have
-shortcuts so that ``sage`` in the console simply works out of the box.  For
-that purpose, follows the steps at the end of the section "Linux".
+After downloading the file, double click on the dmg file to mount it,
+which will take some time.  Then drag the folder ``SageMath`` that
+just appeared to ``/Applications/``.  You might want to have shortcuts
+so that ``sage`` in the console simply works out of the box.  For that
+purpose, follows the steps at the end of the section "Linux".
+
+Alternative macOS binaries are available `here
+<https://github.com/3-manifolds/Sage_macOS/releases/>`_.  These
+have been signed and notarized, eliminating various errors caused by
+Apple's gatekeeper antimalware protections.
+
 
 Microsoft Windows (Cygwin)
 --------------------------

src/sage/symbolic/expression.pyx

@@ -5490,11 +5490,19 @@ cdef class Expression(CommutativeRingElement):
             sage: integrate(f(x), x, 0, a).subs(a=cos(a))
             integrate(f(x), x, 0, cos(a))
 
+        Check that :trac:`31554` is fixed::
+
+            sage: a,b,c,d,x,y = var("a b c d x y")
+            sage: with hold:
+            ....:     print((2*x^0*a + b*y^1).subs({x:c, y:c*d}))
+            b*c*d + 2*a
+
         Check that :trac:`31530` is fixed::
 
             sage: a, b = var("a b")
             sage: (a + b*x).series(x, 2).subs(a=a, b=b)
             (a) + (b)*x + Order(x^2)
+
         """
         cdef dict sdict = {}
         cdef GEx res

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 = '9.3.rc2'
-date = '2021-04-06'
-banner = 'SageMath version 9.3.rc2, Release Date: 2021-04-06'
+version = '9.3.rc3'
+date = '2021-04-12'
+banner = 'SageMath version 9.3.rc3, Release Date: 2021-04-12'