Merge #31764

Author: Matthias Koeppe

.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, 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:
@@ -112,54 +114,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}

.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, 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:
@@ -114,54 +116,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}

.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, 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, 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_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.gitignore

@@ -23,6 +23,14 @@
 /src/environment.yml
 /src/environment-optional.yml
 
+/src/setup.cfg
+/src/requirements.txt
+/src/pyproject.toml
+/src/Pipfile
+/src/Pipfile.lock
+/Pipfile
+/Pipfile.lock
+
 # Various editors
 *~
 
@@ -93,6 +101,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Generated by sage_setup.autogen
+/src/sage/ext/interpreters
+
 # Generated Cython files
 *.so
 src/sage/**/*.c
@@ -103,6 +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
@@ -130,6 +142,14 @@ build/bin/sage-build-env-config
 /build/pkgs/*/src/*.egg-info
 /build/pkgs/*/src/.tox
 
+# Generated by docbuild
+/src/doc/en/reference/*/sage
+/src/doc/en/reference/sage
+/src/doc/en/reference/spkg/*.rst
+/src/doc/output
+/src/doc/en/installation/*.txt
+/src/doc/en/reference/repl/*.txt
+
 # Distribution / packaging
 src/*.egg-info/
 /src/.cython_version
@@ -152,5 +172,8 @@ src/venv.bak/
 
 # tox generated files
 /.tox
+/build/.tox
 /prefix
+
+# git worktree
 worktree*

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.rc5", 
-    "version": "9.3.rc5", 
+    "title": "sagemath/sage: 9.4.beta2", 
+    "version": "9.4.beta2", 
     "upload_type": "software", 
-    "publication_date": "2021-04-30", 
+    "publication_date": "2021-06-19", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc5", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta2", 
             "relation": "isSupplementTo"
         }, 
         {

Pipfile.m4

@@ -0,0 +1,41 @@
+## Pipfile with all packages in the Sage distribution and version information locked
+## FIXME: Many packages still missing.
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+pkgconfig = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pkgconfig/package-version.txt)')"
+cython = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cython/package-version.txt)')"
+pycodestyle = "*"
+ipykernel = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipykernel/package-version.txt)')"
+tox = "*"
+jinja2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../jinja2/package-version.txt)')"
+pytest = "*"
+ipywidgets = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipywidgets/package-version.txt)')"
+sphinx = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../sphinx/package-version.txt)')"
+rope = "*"
+six = "*"
+jupyter-core = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../jupyter_core/package-version.txt)')"
+
+[packages]
+numpy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../numpy/package-version.txt)')"
+cysignals = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cysignals/package-version.txt)')"
+cypari2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cypari/package-version.txt)')"
+gmpy2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../gmpy2/package-version.txt)')"
+psutil = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../psutil/package-version.txt)')"
+pexpect = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pexpect/package-version.txt)')"
+ipython = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipython/package-version.txt)')"
+sympy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../sympy/package-version.txt)')"
+scipy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../scipy/package-version.txt)')"
+pplpy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pplpy/package-version.txt)')"
+matplotlib = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../matplotlib/package-version.txt)')"
+cvxopt = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cvxopt/package-version.txt)')"
+rpy2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../rpy2/package-version.txt)')"
+networkx = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../networkx/package-version.txt)')"
+
+sagemath-standard = { path = "src" }
+
+[requires]
+python_version = "3.9"

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.rc5, Release Date: 2021-04-30
+SageMath version 9.4.beta2, Release Date: 2021-06-19

bootstrap

@@ -24,6 +24,7 @@
 
 # Set SAGE_ROOT to the path to this file and then cd into it
 SAGE_ROOT="$(cd "$(dirname "$0")" && pwd -P)"
+export SAGE_ROOT
 cd "$SAGE_ROOT"
 
 export PATH="$SAGE_ROOT/build/bin:$PATH"
@@ -108,6 +109,10 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
     done
     echo "$spkg_configures" >> m4/sage_spkg_configures.m4
 
+    for pkgname in $(./sage --package list --has-file bootstrap); do
+        (cd build/pkgs/$pkgname && ./bootstrap) || exit 1
+    done
+
     # Default to no filter if "-q" was not passed.
     QUIET_SED_FILTER=""
     if [ "${BOOTSTRAP_QUIET}" = "yes" ]; then
@@ -119,8 +124,6 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
     # ONLY stderr, and to re-output the results back to stderr leaving
     # stdout alone. Basically we swap the two descriptors using a
     # third, filter, and then swap them back.
-    BOOTSTRAP_QUIET="${BOOTSTRAP_QUIET}" \
-    SAGE_ROOT="$SAGE_ROOT" \
     src/doc/bootstrap && \
     install_config_rpath && \
     aclocal -I m4 && \
@@ -262,6 +265,7 @@ do
          ?) usage; exit 2;;
      esac
 done
+export BOOTSTRAP_QUIET
 CONFBALL="upstream/configure-$CONFVERSION.tar.gz"
 
 if [ $DOWNLOAD$SAVE = yesyes ]; then

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 $PKG_NAME"
-
     mkdir -p dist
     rm -f dist/*.whl
     python3 -m pip wheel --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation "$@" || \