Merge #32013

.github/workflows/tox.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, 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, centos-8, gentoo, gentoo-python3.7, 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]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, ubuntu-impish, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, centos-7, centos-8, gentoo, gentoo-python3.7, 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]
         tox_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.beta2", 
-    "version": "9.4.beta2", 
+    "title": "sagemath/sage: 9.4.beta4", 
+    "version": "9.4.beta4", 
     "upload_type": "software", 
-    "publication_date": "2021-06-19", 
+    "publication_date": "2021-07-01", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta2", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta4", 
             "relation": "isSupplementTo"
         }, 
         {

README.md

@@ -9,10 +9,11 @@
 
    https://www.sagemath.org
 
-The Sage Library is GPLv2+, and included packages have [compatible OSS
-licenses](./COPYING.txt). [Over 400 people](https://www.sagemath.org/development-map.html)
-have contributed code to Sage. In many cases, documentation for modules
-and functions list the authors.
+The Sage Library is GPLv2+, and included packages have
+[compatible OSS licenses](./COPYING.txt).
+[Over 400 people](https://www.sagemath.org/development-map.html)
+have contributed code to Sage. In many cases, documentation
+for modules and functions list the authors.
 
 Getting Started
 ---------------
@@ -22,7 +23,7 @@ If you downloaded a [binary](https://www.sagemath.org/download.html)
 Sage is ready to start -- just open a terminal in the directory where
 you extracted the binary archive and type:
 
-    ./sage
+    $ ./sage
 
 (Note that the first run will take more time, as Sage needs to get itself ready.)
 
@@ -118,9 +119,9 @@ virtual appliance](https://wiki.sagemath.org/SageAppliance).
 ------------------------------
 
 Make sure you have installed the most current version of Xcode
-supported on your version of macOS.  If you don't, go to
+supported on your version of macOS.  If you don't, either go to
 https://developer.apple.com/, sign up, and download the free Xcode
-package.
+package, or get it from Apple's app store.
 
 You also need to install the "command line tools": After installing
 Xcode, run `xcode-select --install` from a terminal window; then click
@@ -131,7 +132,7 @@ and then "Install" the Command Line Tools.)
 
 Optionally, you can consider installing Homebrew ("the missing package
 manager for macOS") from https://brew.sh/, which can provide libraries
-such gfortran, gmp, etc.
+such as gfortran, gmp, etc.
 
 Instructions to Build from Source
 ---------------------------------
@@ -173,11 +174,12 @@ Guide](https://doc.sagemath.org/html/en/installation).
 
     - [Git] Alternatively, clone the Sage git repository:
 
-            $ git clone -c core.symlinks=true --branch master https://github.com/sagemath/sage.git
+            $ ORIG=https://github.com/sagemath/sage.git
+            $ git clone -c core.symlinks=true --branch master $ORIG
 
-      This will create the subdirectory `sage`. `cd sage/` and pick the branch you need
-      by doing `git checkout` - typically you want the latest development branch, thus do
-      `git checkout develop`.
+      This will create the subdirectory `sage`. `cd sage/` and pick
+      the branch you need by doing `git checkout` - typically you want
+      the latest development branch, thus do `git checkout develop`.
 
     - [Windows] The Sage source tree contains symbolic links, and the
       build will not work if Windows line endings rather than UNIX
@@ -186,8 +188,8 @@ Guide](https://doc.sagemath.org/html/en/installation).
       Therefore it is crucial that you unpack the source tree from the
       Cygwin (or WSL) `bash` using the Cygwin (or WSL) `tar` utility
       and not using other Windows tools (including mingw). Likewise,
-      when using `git`, it is recommended (but not necessary) to use the Cygwin (or WSL)
-      version of `git`.
+      when using `git`, it is recommended (but not necessary) to use
+      the Cygwin (or WSL) version of `git`.
 
 3. `cd` into the source/build directory:
 
@@ -224,11 +226,16 @@ Guide](https://doc.sagemath.org/html/en/installation).
      avoid having to build Sage's own copy of Python 3.
 
    We have collected lists of system packages that provide these build
-   prerequisites. See [build/pkgs/arch.txt](build/pkgs/arch.txt),
-   [cygwin.txt](build/pkgs/cygwin.txt),
-   [debian.txt](build/pkgs/debian.txt) (also for Ubuntu, Linux Mint,
-   etc.), [fedora.txt](build/pkgs/fedora.txt) (also for Red Hat,
-   CentOS), and [slackware.txt](build/pkgs/slackware.txt).
+   prerequisites. See, in the folder
+   [build/pkgs/_prereq/distros](build/pkgs/_prereq/distros),
+   the files
+   [arch.txt](build/pkgs/_prereq/distros/arch.txt),
+   [cygwin.txt](build/pkgs/_prereq/distros/cygwin.txt),
+   [debian.txt](build/pkgs/_prereq/distros/debian.txt)
+   (also for Ubuntu, Linux Mint, etc.),
+   [fedora.txt](build/pkgs/_prereq/distros/fedora.txt)
+   (also for Red Hat, CentOS), and
+   [slackware.txt](build/pkgs/_prereq/distros/slackware.txt).
 
 7. Optional, but highly recommended: Make sure your system has an SSL
    library and its development files installed.
@@ -245,7 +252,7 @@ Guide](https://doc.sagemath.org/html/en/installation).
 9. Optionally, review the configuration options, which includes
    many optional packages:
 
-        ./configure --help
+        $ ./configure --help
 
 10. Optional, but highly recommended: Set some environment variables to
    customize the build.
@@ -470,7 +477,7 @@ do.
 
 2. (**Obsolete, probably broken**) To make your own source tarball of Sage, type:
 
-       sage --sdist
+        $ sage --sdist
 
    The result is placed in the directory `dist/`.
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.4.beta2, Release Date: 2021-06-19
+SageMath version 9.4.beta4, Release Date: 2021-07-01

build/bin/sage-site

@@ -150,6 +150,7 @@ if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
     # Trac #30002: ensure an English locale so that it is possible to
     # scrape out warnings by pattern matching.
     export LANG=C
+    export LANGUAGE=C
 
     # See #30351: bugs in macOS implementations of openblas/libgopm can cause
     # docbuild to hang if multiple OpenMP threads are allowed.

build/make/Makefile.in

@@ -283,6 +283,11 @@ all-toolchain: base-toolchain
 # given as a prerequisite to any pip-installed packages
 PYTHON_TOOLCHAIN = setuptools pip setuptools_scm wheel setuptools_wheel
 
+# Trac #32056: Avoid installed setuptools leaking into the build of python3 by uninstalling it.
+# It will have to be reinstalled anyway because of its dependency on $(PYTHON).
+python3-SAGE_LOCAL-no-deps: setuptools-clean
+python3-SAGE_VENV-no-deps: setuptools-clean
+
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
 SAGERUNTIME = sagelib $(inst_ipython) $(inst_pexpect) \
@@ -338,23 +343,23 @@ DOC_DEPENDENCIES = sagelib sage_docbuild $(inst_sphinx) \
 doc: doc-html
 
 doc-html: $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+	$(AM_V_at)cd "$(SAGE_SRC)/doc" && sage-logger -p "$(MAKE) doc-html" $(SAGE_ROOT)/logs/dochtml.log
 
 # 'doc-html-no-plot': build docs without building the graphics coming
 # from the '.. plot' directive, in case you want to save a few
 # megabytes of disk space. 'doc-clean' is a prerequisite because the
 # presence of graphics is cached in src/doc/output.
-doc-html-no-plot: doc-clean $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+doc-html-no-plot: doc-clean
+	$(AM_V_at)sage-logger -p "$(MAKE) SAGE_DOCBUILD_OPTS=\"$(SAGE_DOCBUILD_OPTS) --no-plot\" doc-html" $(SAGE_ROOT)/logs/dochtml.log
 
-doc-html-mathjax: $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS)' logs/dochtml.log
+doc-html-mathjax:
+	$(AM_V_at)sage-logger -p "$(MAKE) SAGE_DOCBUILD_OPTS=\"$(SAGE_DOCBUILD_OPTS) -j\" doc-html" $(SAGE_ROOT)/logs/dochtml.log
 
 # Keep target 'doc-html-jsmath' for backwards compatibility.
 doc-html-jsmath: doc-html-mathjax
 
 doc-pdf: $(DOC_DEPENDENCIES)
-	$(AM_V_at)cd ../.. && sage-logger -p './sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS)' logs/docpdf.log
+	$(AM_V_at)cd "$(SAGE_SRC)/doc" && sage-logger -p "$(MAKE) doc-pdf" $(SAGE_ROOT)/logs/docpdf.log
 
 doc-clean: doc-src-clean doc-output-clean
 

build/pkgs/appdirs/SPKG.rst

@@ -0,0 +1,18 @@
+appdirs: A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
+==========================================================================================================
+
+Description
+-----------
+
+A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
+
+License
+-------
+
+MIT
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/appdirs/
+

build/pkgs/appdirs/checksums.ini

@@ -0,0 +1,5 @@
+tarball=appdirs-VERSION.tar.gz
+sha1=1fa04e44b1084338cb7b21e9cf44fce5efb81840
+md5=d6bca12613174185dd9abc8a29f4f012
+cksum=1191718163
+upstream_url=https://pypi.io/packages/source/a/appdirs/appdirs-VERSION.tar.gz

build/pkgs/appdirs/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/appdirs/install-requires.txt

@@ -0,0 +1 @@
+appdirs

build/pkgs/appdirs/package-version.txt

@@ -0,0 +1 @@
+1.4.4

build/pkgs/appdirs/spkg-configure.m4

@@ -0,0 +1,7 @@
+SAGE_SPKG_CONFIGURE([appdirs], [
+    sage_spkg_install_appdirs=yes
+  ], [dnl REQUIRED-CHECK
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_VIRTUALENV])
+    dnl only needed as a dependency of virtualenv.
+    AS_VAR_SET([SPKG_REQUIRE], [$sage_spkg_install_virtualenv])
+  ])

build/pkgs/appdirs/spkg-install.in

@@ -0,0 +1,2 @@
+cd src
+sdh_pip_install .

build/pkgs/appdirs/type

@@ -0,0 +1 @@
+standard

build/pkgs/babel/checksums.ini

@@ -1,4 +1,5 @@
 tarball=Babel-VERSION.tar.gz
-sha1=6aed99e4fb8a2a75de7815599f610cdcbb81e3c2
-md5=c384ac03026e8fe6f9b90f55201f1bff
-cksum=3805303136
+sha1=1ce15f82eba5184cabe6ac1491cb58262e27adfd
+md5=7166099733d78aa857d74fa50d8ff58c
+cksum=1695340328
+upstream_url=https://pypi.io/packages/source/b/babel/Babel-VERSION.tar.gz

build/pkgs/babel/package-version.txt

@@ -1 +1 @@
-2.6.0
+2.9.1

build/pkgs/brial/spkg-configure.m4

@@ -1,13 +1,13 @@
 SAGE_SPKG_CONFIGURE([brial], [
   dnl Trac #31624: Avoid C++ ABI issues
-  SAGE_SPKG_DEPCHECK([gcc boost m4ri], [
+  SAGE_SPKG_DEPCHECK([gcc boost_cropped m4ri], [
     # If we're using the system m4ri and boost, ensure that we can
     # compile and run an executable linked against both libbrial and
     # libbrial_groebner (both are used by SageMath).
     AC_LANG_PUSH(C++)
     SAVED_LIBS=$LIBS
     LIBS="$LIBS -lbrial -lbrial_groebner"
-    AC_MSG_CHECKING([if we can link against brial libraries])
+    AC_MSG_CHECKING([if we can link against brial libraries and run])
     AC_RUN_IFELSE([
       AC_LANG_PROGRAM([
         #include <polybori.h>
@@ -48,11 +48,43 @@ SAGE_SPKG_CONFIGURE([brial], [
 	  ], [
           AC_MSG_RESULT([yes])
           sage_spkg_install_brial=no
-      ])
+      ], [AC_MSG_RESULT([cross compiling. Assume yes])
+          sage_spkg_install_brial=no])
     ],
     [
       AC_MSG_RESULT([no])
       sage_spkg_install_brial=yes
+    ],
+    [
+     AC_MSG_CHECKING([if we can link against brial libraries])
+     AC_LINK_IFELSE([
+       AC_LANG_PROGRAM([
+         #include <polybori.h>
+         #include <polybori/groebner/groebner_alg.h>
+         USING_NAMESPACE_PBORI
+         USING_NAMESPACE_PBORIGB
+
+     class MyConstant : public BooleConstant{
+           public: void negate() { this->m_value = !this->m_value; }
+         };
+       ],[
+         BoolePolyRing r = BoolePolyRing(2, COrderEnums::dlex);
+         ReductionStrategy rs = ReductionStrategy(r);
+         rs.llReduceAll(); // uses groebner lib
+         if (2 != r.nVariables()) { return 1; }
+         if (r.constant(true) == r.constant(false)) { return 2; }
+         MyConstant f = MyConstant();
+         f.negate(); // ensures v1.1.0+ if m_value isn't const
+         if (!f.isOne()) { return 3; }
+         return 0;
+       ])
+       ],[
+         AC_MSG_RESULT([yes])
+         sage_spkg_install_brial=yes
+       ],[
+         AC_MSG_RESULT([no])
+         sage_spkg_install_brial=no
+       ])
     ])
     LIBS=$SAVED_LIBS
     AC_LANG_POP

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=9dab15e2209bd5515c3822aeb6beb911dc9a6084
-md5=e76f8e7f8be26c9729dd010f1a93c245
-cksum=641170247
+sha1=7b88d740d7ed702c15cb4048ae08c2faf2e9852c
+md5=6252f2920838a7ea42b17845aa9782a2
+cksum=2536572108

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-8b70b5bba76ffd6bd0f1c2441afc249f5046a612
+06ec5d949d4ac37fffbebba5ab2ad5294cb141e1

build/pkgs/curl/spkg-configure.m4

@@ -20,7 +20,12 @@ SAGE_SPKG_CONFIGURE([curl], [
 
            AC_RUN_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[
              curl_easy_setopt(NULL,CURLOPT_URL,NULL);
-           ]])], sage_libcurl_cv_lib_curl_executable=yes, sage_libcurl_cv_lib_curl_executable=no)
+           ]])], sage_libcurl_cv_lib_curl_executable=yes, sage_libcurl_cv_lib_curl_executable=no, [
+              dnl cross compiling. link only
+              AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[
+               curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+             ]])], sage_libcurl_cv_lib_curl_executable=yes, sage_libcurl_cv_lib_curl_executable=no)]
+           )
       ])
     AS_IF([test "$sage_libcurl_cv_lib_curl_executable" = "no"], [sage_spkg_install_curl=yes])
 ])

build/pkgs/distlib/SPKG.rst

@@ -0,0 +1,18 @@
+distlib: Distribution utilities
+===============================
+
+Description
+-----------
+
+Distribution utilities
+
+License
+-------
+
+Python license
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/distlib/
+

build/pkgs/distlib/checksums.ini

@@ -0,0 +1,5 @@
+tarball=distlib-VERSION.zip
+sha1=1c575431e31c32d25596c360e81bba7fe4638669
+md5=4baf787d8aceb260d6f77cb31bf27cf6
+cksum=2902365751
+upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.zip

build/pkgs/distlib/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/distlib/install-requires.txt

@@ -0,0 +1 @@
+distlib

build/pkgs/distlib/package-version.txt

@@ -0,0 +1 @@
+0.3.1

build/pkgs/distlib/spkg-configure.m4

@@ -0,0 +1,7 @@
+SAGE_SPKG_CONFIGURE([distlib], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_VIRTUALENV])
+    sage_spkg_install_distlib=yes
+  ], [dnl REQUIRED-CHECK
+    dnl only needed as a dependency of virtualenv.
+    AS_VAR_SET([SPKG_REQUIRE], [$sage_spkg_install_virtualenv])
+  ])

build/pkgs/distlib/spkg-install.in

@@ -0,0 +1,2 @@
+cd src
+sdh_pip_install .

build/pkgs/distlib/type

@@ -0,0 +1 @@
+standard

build/pkgs/docutils/checksums.ini

@@ -1,4 +1,5 @@
 tarball=docutils-VERSION.tar.gz
-sha1=32cefb69ac3dab5b04c4d150776f35419cc4c863
-md5=c53768d63db3873b7d452833553469de
-cksum=2981697109
+sha1=f423535c12fcd2a68d4fc52525fbe36020a58ab5
+md5=ed810564c25063e9dac10dd0893ead47
+cksum=3160620183
+upstream_url=https://pypi.io/packages/source/d/docutils/docutils-VERSION.tar.gz