Merge tag '9.5.beta3' into t/32442/__configure__make___with_sage_venv…

…_the_default SageMath version 9.5.beta3, Release Date: 2021-10-11
sagemath · Oct 11, 2021 · e33bc89 · e33bc89
2 parents dcb4a08 + c896669
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diff --git a/.github/workflows/tox-experimental.yml b/.github/workflows/tox-experimental.yml
@@ -40,7 +40,8 @@ jobs:
       matrix:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
-        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
+        # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

diff --git a/.github/workflows/tox-optional.yml b/.github/workflows/tox-optional.yml
@@ -40,7 +40,8 @@ jobs:
       matrix:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
-        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
+        # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta2", 
-    "version": "9.5.beta2", 
+    "title": "sagemath/sage: 9.5.beta3", 
+    "version": "9.5.beta3", 
     "upload_type": "software", 
-    "publication_date": "2021-09-26", 
+    "publication_date": "2021-10-11", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta2", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta3", 
             "relation": "isSupplementTo"
         }, 
         {

diff --git a/COPYING.txt b/COPYING.txt
@@ -32,7 +32,6 @@ the licenses of the components of Sage are included below as well.
 SOFTWARE                    LICENSE
 -----------------------------------------------------------------------
 arb                         GPLv2+
-atlas                       Modified BSD
 boehm_gc                    MIT-like license (see below)
 backports_ssl_match_hostname  Python License
 boost_cropped               Boost Software License (see below)

diff --git a/README.md b/README.md
@@ -349,7 +349,7 @@ Simplified directory layout (only essential files/directories):
 SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 ├── build
 │   └── pkgs              Every package is a subdirectory here
-│       ├── atlas
+│       ├── 4ti2
 │       …
 │       └── zn_poly
 ├── configure             Top-level configure script
@@ -381,9 +381,9 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 │   ├── dochtml.log       Log of the documentation build
 │   ├── install.log       Full install log
 │   └── pkgs              Build logs of individual packages
-│       ├── atlas-3.10.1.p7.log
+│       ├── alabaster-0.7.12.log
 │       …
-│       └── zn_poly-0.9.p11.log
+│       └── zn_poly-0.9.2.log
 ├── m4                    M4 macros for configure
 │   └── *.m4
 ├── Makefile              Running "make" uses this file
@@ -394,9 +394,9 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 │   ├── doc               Sage documentation sources
 │   └── sage              The Sage library source code
 ├── upstream              Source tarballs of packages
-│   ├── atlas-3.10.1.tar.bz2
+│   ├── Babel-2.9.1.tar.gz
 │   …
-│   └── zn_poly-0.9.tar.bz2
+│   └── zn_poly-0.9.2.tar.gz
 └── VERSION.txt
 ```
 For more details see [our Developer's Guide](https://doc.sagemath.org/html/en/developer/coding_basics.html#files-and-directory-structure).

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 9.5.beta2, Release Date: 2021-09-26
+SageMath version 9.5.beta3, Release Date: 2021-10-11
diff --git a/build/bin/sage-package b/build/bin/sage-package
@@ -16,7 +16,6 @@
 #   $ sage-package list | sort
 #   4ti2
 #   arb
-#   atlas
 #   autotools
 #   [...]
 #   zn_poly

diff --git a/build/make/Makefile.in b/build/make/Makefile.in
@@ -33,7 +33,7 @@ SPKG_INST_RELDIR = var/lib/sage/installed
 TOOLCHAIN = @SAGE_TOOLCHAIN@
 PYTHON = python3
 MP_LIBRARY = @SAGE_MP_LIBRARY@
-BLAS = @SAGE_BLAS@
+BLAS = openblas
 
 # pkgconfig files generated/installed at build time
 PCFILES = @SAGE_SYSTEM_FACADE_PC_FILES@

diff --git a/build/pkgs/4ti2/distros/arch.txt b/build/pkgs/4ti2/distros/arch.txt
@@ -0,0 +1 @@
+4ti2
diff --git a/build/pkgs/4ti2/distros/cygwin.txt b/build/pkgs/4ti2/distros/cygwin.txt
@@ -0,0 +1 @@
+lib4ti2-devel
diff --git a/build/pkgs/4ti2/distros/debian.txt b/build/pkgs/4ti2/distros/debian.txt
@@ -0,0 +1 @@
+4ti2
diff --git a/build/pkgs/4ti2/distros/fedora.txt b/build/pkgs/4ti2/distros/fedora.txt
@@ -0,0 +1 @@
+4ti2
diff --git a/build/pkgs/4ti2/distros/freebsd.txt b/build/pkgs/4ti2/distros/freebsd.txt
@@ -0,0 +1 @@
+math/4ti2
diff --git a/build/pkgs/4ti2/distros/gentoo.txt b/build/pkgs/4ti2/distros/gentoo.txt
@@ -0,0 +1 @@
+sci-mathematics/4ti2
diff --git a/build/pkgs/4ti2/spkg-configure.m4 b/build/pkgs/4ti2/spkg-configure.m4
@@ -0,0 +1,32 @@
+SAGE_SPKG_CONFIGURE([4ti2], [
+    SAGE_SPKG_DEPCHECK([gmp mpir glpk zlib], [
+        dnl Debian installs these programs with an executable prefix "4ti2-",
+        dnl OpenSUSE uses the prefix "4ti2_".
+        dnl Singular checks for unprefixed and prefixed with "4ti2-".
+        dnl Polymake does not check for prefixed binaries.
+        m4_foreach([prog], [hilbert,markov,graver,zsolve,qsolve,rays,ppi,circuits,groebner], [
+            AC_CHECK_PROGS([FOURTITWO_]m4_toupper(prog), prog [4ti2-]prog [4ti2_]prog)
+            AS_VAR_IF([FOURTITWO_]m4_toupper(prog), [""], [sage_spkg_install_4ti2=yes])
+            AC_SUBST([FOURTITWO_]m4_toupper(prog))
+        ])
+        dnl Adapted from https://github.com/latte-int/latte/blob/master/m4/4ti2-check.m4
+        AC_MSG_CHECKING(for library 4ti2gmp)
+        BACKUP_CXXFLAGS=${CXXFLAGS}
+        BACKUP_LIBS=${LIBS}
+        FORTYTWO_CXXFLAGS="-D__STDC_LIMIT_MACROS -D_4ti2_GMP_"
+        FORTYTWO_LIBS="-l4ti2gmp -lzsolve"
+        CXXFLAGS="${BACKUP_CXXFLAGS} ${FORTYTWO_CXXFLAGS} ${GMP_CFLAGS}"
+        LIBS="${BACKUP_LIBS} ${FORTYTWO_LIBS} ${GMP_LIBS}"
+        AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+#include "4ti2/4ti2.h"
+]], [[ _4ti2_rays_create_state(_4ti2_PREC_INT_ARB);
+]])],[
+        AC_MSG_RESULT([yes])
+],[
+        AC_MSG_RESULT([no])
+        sage_spkg_install_4ti2=yes
+])
+        CXXFLAGS=${BACKUP_CXXFLAGS}
+        LIBS=${BACKUP_LIBS}
+    ])
+])
diff --git a/build/pkgs/_bootstrap/distros/void.txt b/build/pkgs/_bootstrap/distros/void.txt
@@ -1,4 +1,4 @@
 # Packages needed for ./bootstrap
-gettext autoconf automake libtool pkg-config
+gettext autoconf automake libtool
 gettext-devel
 xtools mk-configure
diff --git a/build/pkgs/_prereq/distros/void.txt b/build/pkgs/_prereq/distros/void.txt
@@ -2,6 +2,7 @@ binutils
 make
 m4
 perl
+pkg-config
 python3
 tar
 bc

diff --git a/build/pkgs/arb/distros/void.txt b/build/pkgs/arb/distros/void.txt
@@ -0,0 +1 @@
+arb-devel
diff --git a/build/pkgs/argcomplete/SPKG.rst b/build/pkgs/argcomplete/SPKG.rst
@@ -0,0 +1,18 @@
+argcomplete: Bash tab completion for argparse
+=============================================
+
+Description
+-----------
+
+Bash tab completion for argparse
+
+License
+-------
+
+Apache Software License
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/argcomplete/
+
diff --git a/build/pkgs/argcomplete/checksums.ini b/build/pkgs/argcomplete/checksums.ini
@@ -0,0 +1,5 @@
+tarball=argcomplete-VERSION.tar.gz
+sha1=bd6b35aee6fc44c82d02772b054b5c5ff1bc5983
+md5=ded03f9c5d41c193dfe5869634d78211
+cksum=3352024634
+upstream_url=https://pypi.io/packages/source/a/argcomplete/argcomplete-VERSION.tar.gz
diff --git a/build/pkgs/scandir/dependencies → build/pkgs/argcomplete/dependencies b/build/pkgs/scandir/dependencies → build/pkgs/argcomplete/dependencies
@@ -2,4 +2,3 @@ $(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 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.
diff --git a/build/pkgs/argcomplete/install-requires.txt b/build/pkgs/argcomplete/install-requires.txt
@@ -0,0 +1 @@
+argcomplete
diff --git a/build/pkgs/argcomplete/package-version.txt b/build/pkgs/argcomplete/package-version.txt
@@ -0,0 +1 @@
+1.12.3
diff --git a/build/pkgs/argcomplete/spkg-install.in b/build/pkgs/argcomplete/spkg-install.in
@@ -0,0 +1,2 @@
+cd src
+sdh_pip_install .
diff --git a/build/pkgs/atlas/type → build/pkgs/argcomplete/type b/build/pkgs/atlas/type → build/pkgs/argcomplete/type
diff --git a/build/pkgs/atlas/SPKG.rst b/build/pkgs/atlas/SPKG.rst
diff --git a/build/pkgs/atlas/checksums.ini b/build/pkgs/atlas/checksums.ini