Merge tag '9.4.beta4' into t/31280/jupyter_upgrade

SageMath version 9.4.beta4, Release Date: 2021-07-01

.github/workflows/lint.yml

@@ -30,7 +30,7 @@ jobs:
     - name: Install relint
       run: pip install tox relint
     - name: Lint using relint
-      run: tox -e relint src/
+      run: tox -e relint src/sage/
   lint-pyright:
     name: Static type check with pyright
     runs-on: ubuntu-latest

.github/workflows/tox-experimental.yml

@@ -38,7 +38,9 @@ jobs:
       fail-fast: false
       max-parallel: 6
       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, 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]
+        # 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]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.github/workflows/tox-optional.yml

@@ -38,7 +38,9 @@ jobs:
       fail-fast: false
       max-parallel: 6
       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, 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]
+        # 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]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.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 }}

.gitignore

@@ -114,6 +114,7 @@ src/sage/modular/arithgroup/farey_symbol.h
 !src/sage/graphs/cliquer/cl.c
 !src/sage/graphs/graph_decompositions/sage_tdlib.cpp
 !src/sage/libs/eclib/wrap.cpp
+!src/sage/libs/linkages/padics/relaxed/flint_helper.c
 !src/sage/misc/inherit_comparison_impl.c
 !src/sage/modular/arithgroup/farey.cpp
 !src/sage/modular/arithgroup/sl2z.cpp

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.beta0", 
-    "version": "9.4.beta0", 
+    "title": "sagemath/sage: 9.4.beta4", 
+    "version": "9.4.beta4", 
     "upload_type": "software", 
-    "publication_date": "2021-05-25", 
+    "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.beta0", 
+            "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.beta0, Release Date: 2021-05-25
+SageMath version 9.4.beta4, Release Date: 2021-07-01

build/bin/sage-bootstrap-python

@@ -30,6 +30,15 @@ fi
 # is accessible by this python; this is to guard on Cygwin against Pythons
 # installed somewhere else in Windows.
 
+# 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.
+
+if [ "$LC_ALL" = "C" -o "$LANG" = "C" -o "$LC_CTYPE" = "C" ]; then
+    LC_ALL=$(locale -a | grep -E -i '^(c|en_us)[-.]utf-?8$' | head -n 1)
+    LANG=$LC_ALL
+    export LC_ALL
+    export LANG
+fi
 
 PYTHONS="python python3 python3.8 python3.7 python2.7 python3.6 python2"
 for PY in $PYTHONS; do

build/bin/sage-dist-helpers

@@ -39,10 +39,10 @@
 #
 # - sdh_configure [...]
 #
-#    Runs `./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"`,
-#    (for autoconf'd projects with extra
-#        --disable-maintainer-mode --disable-dependency-tracking)
-#    Additional arguments to `./configure` may be given as arguments.
+#    Runs `./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"`
+#    --disable-static, (for autoconf'd projects with extra
+#    --disable-maintainer-mode --disable-dependency-tracking) Additional
+#    arguments to `./configure` may be given as arguments.
 #
 # - sdh_make [...]
 #
@@ -160,9 +160,16 @@ sdh_configure() {
     if [ -z "$CONFIG_SHELL" ]; then
         export CONFIG_SHELL=`command -v bash`
     fi
-    ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" --disable-maintainer-mode --disable-dependency-tracking "$@"
+    if [ "$UNAME" = "CYGWIN" ]; then
+        # TODO: To use --disable-static for all packages on Cygwin, need
+        # #30814: Cygwin: Fix remaining packages to build shared libraries, using AM_LDFLAGS=-no-undefined
+        DISABLE_STATIC=
+    else
+        DISABLE_STATIC=--disable-static
+    fi
+    ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" $DISABLE_STATIC --disable-maintainer-mode --disable-dependency-tracking "$@"
     if [ $? -ne 0 ]; then # perhaps it is a non-autoconf'd project
-      ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" "$@"
+      ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" $DISABLE_STATIC "$@"
       if [ $? -ne 0 ]; then
         if [ -f "$(pwd)/config.log" ]; then
             sdh_die <<_EOF_
@@ -211,14 +218,6 @@ sdh_setup_bdist_wheel() {
 
 sdh_pip_install() {
     echo "Installing $PKG_NAME"
-    if [ -n "$SAGE_DESTDIR" ]; then
-        local sudo=""
-    else
-        local sudo="$SAGE_SUDO"
-    fi
-    $sudo sage-pip-uninstall "$@" || \
-        echo 2>&1 "Warning: Failure trying to uninstall a previous version of $PKG_NAME"
-
     mkdir -p dist
     rm -f dist/*.whl
     python3 -m pip wheel --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation "$@" || \

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