Merge branch 'develop' into partition-libgap-class-fcn

.ci/build-docker.sh

@@ -26,7 +26,7 @@ docker_build() {
     # Docker's --cache-from does not really work with multi-stage builds: https://github.com/moby/moby/issues/34715
     # So we just have to rely on the local cache.
     time docker build -f docker/Dockerfile \
---build-arg "--build-arg "MAKEFLAGS=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS=${SAGE_NUM_THREADS}" --build-arg "MAKEFLAGS_DOCBUILD=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS_DOCBUILD=${SAGE_NUM_THREADS_DOCBUILD}" --build-arg ARTIFACT_BASE=$ARTIFACT_BASE $@
+--build-arg "MAKEFLAGS=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS=${SAGE_NUM_THREADS}" --build-arg "MAKEFLAGS_DOCBUILD=${MAKEFLAGS}" --build-arg "SAGE_NUM_THREADS_DOCBUILD=${SAGE_NUM_THREADS_DOCBUILD}" --build-arg ARTIFACT_BASE=$ARTIFACT_BASE $@
 }
 
 # We use a multi-stage build /docker/Dockerfile. For the caching to be
@@ -53,7 +53,7 @@ docker tag "$DOCKER_IMAGE_CLI" "$DOCKER_IMAGE_BINDER"
 # Display the layers of this image
 docker history "$DOCKER_IMAGE_CLI"
 # Build the developer image with the build artifacts intact.
-# Note: It's important to build the dev image last because it might be tagged as ARTIFACT_BASE.
+# Note: It is important to build the dev image last because it might be tagged as ARTIFACT_BASE.
 docker_build --target sagemath-dev --tag "$DOCKER_IMAGE_DEV" .
 # Display the layers of this image
 docker history "$DOCKER_IMAGE_DEV"

.ci/update-env.sh

@@ -27,8 +27,6 @@ if [ -n "$CI_MONKEY_PATCH" ]; then
     $SCRIPT
 fi
 
-WITH_PYTHON=${WITH_PYTHON:-2}
-
 # From the docker documentation: "A tag name must be valid ASCII and may
 # contain lowercase and uppercase letters, digits, underscores, periods and
 # dashes. A tag name may not start with a period or a dash and may contain a
@@ -38,10 +36,6 @@ export DOCKER_TAG=`echo $DOCKER_TAG | tr -d '[:space:]' | tr -c '[:alnum:]_.-' '
 [[ -z "$DOCKER_TAG" ]] && export DOCKER_TAG=none
 [[ "$DOCKER_TAG" = "master" ]] && export DOCKER_TAG=latest
 
-if [ $WITH_PYTHON = 3 ]; then
-    export DOCKER_TAG=${DOCKER_TAG}-py3
-fi
-
 export DOCKER_IMAGE_CLI=${DOCKER_NAMESPACE:-sagemath}/sagemath:$DOCKER_TAG
 export DOCKER_IMAGE_DEV=${DOCKER_NAMESPACE:-sagemath}/sagemath-dev:$DOCKER_TAG
 

.github/workflows/tox.yml

@@ -239,13 +239,13 @@ jobs:
         if: contains(matrix.tox_system_factor, 'nobootstrap')
       - name: Move homebrew away
         run: |
-          (cd /usr/local && for a in bin etc include lib opt sbin share; do mv $a $a-moved; done)
+          (cd /usr/local && for a in bin etc include lib opt sbin share; do sudo mv $a $a-moved; done)
       - name: Select Xcode version
         run: |
           if [ ${{ matrix.xcode_version_factor }} != default ]; then sudo xcode-select -s /Applications/Xcode_${{ matrix.xcode_version_factor }}.app; fi
       - name: Install test prerequisites
         run: |
-          /usr/bin/python3 -m pip install --user tox
+          sudo /usr/bin/python3 -m pip install tox
       - name: Install python3 from python.org
         # As of 2020-03-30 (https://github.com/actions/virtual-environments/blob/master/images/macos/macos-10.15-Readme.md),
         # Python 3.7.7 is installed on GitHub Actions runners.  But we install our own copy from the python.org binary package.

.gitignore

@@ -4,9 +4,7 @@
 /logs
 /upstream
 
-#############################
-# Autotools generated files #
-#############################
+# Autotools generated files
 /aclocal.m4
 /autom4te.cache/
 /config/
@@ -20,10 +18,6 @@
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig
 
-###################
-# Temporary Files #
-###################
-
 # Various editors
 *~
 
@@ -43,7 +37,7 @@
 .iml
 
 # VSCode
-.vscode
+.vscode/*
 
 # XCode
 xcuserdata/
@@ -77,40 +71,79 @@ $RECYCLE.BIN/
 # SublimeText
 *.sublime-workspace
 
-#################
-# SageMathCloud #
-#################
+# SageMathCloud
 *.sage-chat
 *.sage-history
 *.syncdoc*
 
-###########
-# Jupyter #
-###########
+# Jupyter
 .ipynb_checkpoints
 Untitled*.ipynb
 
-#############################
-# GitLab CI generated files #
-#############################
+# GitLab CI generated files
 gitlab-build-docker.log
 
-/src/.cython_version
-/src/build
-/src/Makefile
-/src/bin/sage-env-config
-/build/bin/sage-build-env-config
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Generated Cython files
+*.so
+src/sage/**/*.c
+src/sage/**/*.cpp
+src/sage/modular/arithgroup/farey_symbol.h
+!src/sage/cpython/debugimpl.c
+!src/sage/graphs/base/boost_interface.cpp
+!src/sage/graphs/cliquer/cl.c
+!src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp
+!src/sage/libs/eclib/wrap.cpp
+!src/sage/misc/inherit_comparison_impl.c
+!src/sage/modular/arithgroup/farey.cpp
+!src/sage/modular/arithgroup/sl2z.cpp
+!src/sage/rings/bernmm/bern_modp.cpp
+!src/sage/rings/bernmm/bern_modp_util.cpp
+!src/sage/rings/bernmm/bern_rat.cpp
+!src/sage/rings/bernmm/bernmm-test.cpp
+!src/sage/rings/padics/transcendantal.c
+!src/sage/rings/polynomial/weil/power_sums.c
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+!src/sage/stats/distributions/dgs_bern.c
+!src/sage/stats/distributions/dgs_gauss_dp.c
+!src/sage/stats/distributions/dgs_gauss_mp.c
+
+# Temporary build files
+build/temp.*/
+build/bin/sage-build-env-config
 
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST
 /build/pkgs/*/src/*.egg-info
 /build/pkgs/*/src/.tox
 
-#######################
-# tox generated files #
-#######################
+# Distribution / packaging
+src/*.egg-info/
+/src/.cython_version
+/src/build
+/src/Makefile
+/src/bin/sage-env-config
+
+# Virtual environments
+src/.env
+src/.venv
+src/env/
+src/venv/
+src/ENV/
+src/env.bak/
+src/venv.bak/
+
+# mypy
+**/.mypy_cache/
 
+# tox generated files
 /.tox
 /prefix
 worktree*

.homebrew-build-env

@@ -2,7 +2,7 @@
 # that activate keg-only homebrew package installations
 
 HOMEBREW=`brew --prefix` || return 1
-for l in gettext bzip2; do
+for l in gettext bzip2 texinfo; do
     if [ -d "$HOMEBREW/opt/$l/bin" ]; then
         PATH="$HOMEBREW/opt/$l/bin:$PATH"
     fi

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.2.rc3", 
-    "version": "9.2.rc3", 
+    "title": "sagemath/sage: 9.3.beta1", 
+    "version": "9.3.beta1", 
     "upload_type": "software", 
-    "publication_date": "2020-10-18", 
+    "publication_date": "2020-11-07", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.2.rc3", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta1", 
             "relation": "isSupplementTo"
         }, 
         {

README.md

@@ -173,9 +173,11 @@ Guide](https://doc.sagemath.org/html/en/installation).
 
     - [Git] Alternatively, clone the Sage git repository:
 
-            $ git clone -c core.symlinks=true --branch master git://trac.sagemath.org/sage.git
+            $ git clone -c core.symlinks=true --branch master https://github.com/sagemath/sage.git
 
-      This will create the subdirectory `sage`.
+      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

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.2.rc3, Release Date: 2020-10-18
+SageMath version 9.3.beta1, Release Date: 2020-11-07

bootstrap

@@ -256,13 +256,6 @@ MAKE_SILENT=""
 $MAKE ${MAKE_SILENT} bootstrap-clean 2>/dev/null
 mkdir config 2>/dev/null
 
-# If Sage has not been built yet, this will fail due to a missing
-# sage-env-config.
-if [ -f src/bin/sage-env-config ]; then
-    . src/bin/sage-env-config
-    . src/bin/sage-env
-fi
-
 if [ $ALWAYSDOWNLOAD = yes ]; then
     if [ -n "$CONFTARBALL_URL" ]; then
         URL="$CONFTARBALL_URL"/configure-$CONFVERSION.tar.gz

build/bin/sage-clone-source

@@ -35,6 +35,7 @@ git clone "$SRC" "$DST"
 
 cd "$DST"
 git remote set-url origin "$SAGE_REPO_ANONYMOUS"
+git remote set-url --push origin "$SAGE_REPO_AUTHENTICATED"
 
 # Save space
 git gc --aggressive --prune=now

build/bin/sage-guess-package-system

@@ -3,7 +3,7 @@
 # First test for user-installable package systems, then system package systems
 if conda --version > /dev/null 2>&1; then
     if [ -z "$CONDA_DEFAULT_ENV" ]; then
-        echo >&2 -n "(ignoring conda because no environment is active) "
+        printf >&2 "(ignoring conda because no environment is active) "
     else
         echo conda
         exit

build/bin/sage-spkg

@@ -489,6 +489,7 @@ export SAGE_ROOT="$SAGE_ROOT"
 export SAGE_SRC="$SAGE_SRC"
 export SAGE_PKG_DIR="$script_dir"
 export SAGE_SPKG_SCRIPTS="$SAGE_SPKG_SCRIPTS"
+export SAGE_SPKG_WHEELS="$SAGE_SPKG_WHEELS"
 
 export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"

build/bin/sage-spkg-info

@@ -40,7 +40,7 @@ for system_package_file in "$PKG_DISTROS"/*.txt; do
                 echo "$system:"
                 ;;
         esac
-        echo -n "  "
+        printf "  "
         sage-print-system-package-command $system --prompt --sudo install $system_packages
     fi
 done

build/bin/write-dockerfile.sh

@@ -17,8 +17,8 @@ for PKG_SCRIPTS in build/pkgs/*; do
     if [ -d $PKG_SCRIPTS ]; then
         PKG_BASE=$(basename $PKG_SCRIPTS)
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/$SYSTEM.txt
-        PKG_TYPE=$(cat $PKG_SCRIPTS/type)
-        if [ -f $SYSTEM_PACKAGES_FILE -a -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+        if [ -f $PKG_SCRIPTS/type -a -f $SYSTEM_PACKAGES_FILE -a -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+           PKG_TYPE=$(cat $PKG_SCRIPTS/type)
            PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
            if [ -n "PKG_SYSTEM_PACKAGES" ]; then
                case "$PKG_TYPE" in

build/pkgs/_recommended/SPKG.txt

@@ -0,0 +1,6 @@
+= _recommended =
+
+== Description ==
+
+Script package representing a list of system packages recommended
+to be installed for additional functionality.

build/pkgs/_recommended/distros/debian.txt

@@ -0,0 +1,17 @@
+# From https://wiki.sagemath.org/prerequisitesUbuntu
+
+# to generate pdf documentation
+texlive-generic-extra
+# to convert Jupyter notebooks to pdf
+texlive-xetex
+# to generate pdf documentation
+latexmk
+# to convert Jupyter notebooks to pdf
+pandoc
+# to render text with LaTeX in Matplotlib
+dvipng
+# to run the Jmol 3D viewer from the console and generate images for 3D plots in the documentation
+default-jdk
+# to produce animations
+ffmpeg
+libavdevice-dev

build/pkgs/_recommended/distros/homebrew.txt

@@ -0,0 +1,8 @@
+# To convert Jupyter notebooks to pdf:
+pandoc
+# To produce animations:
+ffmpeg
+imagemagick
+# Homebrew's texinfo can be used to build the info files for ecl and
+# maxima but the OS X default version of texinfo cannot.
+texinfo

build/pkgs/_recommended/spkg-configure.m4

@@ -0,0 +1,3 @@
+SAGE_SPKG_CONFIGURE([_recommended], [
+  sage_spkg_install__recommended=yes
+])

build/pkgs/_recommended/spkg-install

@@ -0,0 +1,2 @@
+#! /usr/bin/env bash
+# Nothing to do

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f724be3bb37dd71f5b07dc1b4542a4ad23461e47
-md5=2a25fb97ee7e9c9eaa85cdc6e1082a2e
-cksum=1804502685
+sha1=13ac5ae7fa66fb0f1dc4fb09b4c5c6d72918a3ef
+md5=67b20028087b39225833e6a7fe2553fe
+cksum=832894188

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-70d165564b827f40db047c1ce0f18aed56c4ad1b
+8e72e1b9c9b3e9b84c29245666493e0a1bd48cab

build/pkgs/deformation/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/fplll/distros/conda.txt

@@ -0,0 +1 @@
+fplll