Merge tag '9.2.beta5' into t/28197/public/ticket/28197-reb

SageMath version 9.2.beta5, Release Date: 2020-07-12

.gitattributes

@@ -0,0 +1,5 @@
+# Force LF normalization
+* text=auto eol=lf
+# except for Windows batch files
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf

.github/workflows/ci-cygwin-minimal.yml

@@ -11,7 +11,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   SAGE_CHECK: warn
-  SAGE_CHECK_PACKAGES: "!cython,!r,!python3,!python2,!nose,!pathpy,!gap,!cysignals,!linbox,!git,!ppl"
+  SAGE_CHECK_PACKAGES: "!cython,!r,!python3,!nose,!pathpy,!gap,!cysignals,!linbox,!git,!ppl"
   CYGWIN: winsymlinks:native
   CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url
   SAGE_FAT_BINARY: yes
@@ -94,7 +94,7 @@ jobs:
   cygwin-stage-i-b:
     env:
       STAGE: i-b
-      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi singledispatch pkgconfig pplpy
+      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi pkgconfig pplpy
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/ci-cygwin-standard.yml

@@ -11,7 +11,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   SAGE_CHECK: warn
-  SAGE_CHECK_PACKAGES: "!cython,!r,!python3,!python2,!nose,!pathpy,!gap,!cysignals,!linbox,!git,!ppl"
+  SAGE_CHECK_PACKAGES: "!cython,!r,!python3,!nose,!pathpy,!gap,!cysignals,!linbox,!git,!ppl"
   CYGWIN: winsymlinks:native
   CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url
   SAGE_FAT_BINARY: yes
@@ -94,7 +94,7 @@ jobs:
   cygwin-stage-i-b:
     env:
       STAGE: i-b
-      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi singledispatch pkgconfig pplpy
+      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi pkgconfig pplpy
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/tox-gcc_spkg.yml

@@ -1,4 +1,4 @@
-name: Run SAGE_ROOT/tox.ini
+name: Test Linux --without-system-gcc
 
 ## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with select environments,
 ## whenever a GitHub pull request is opened or synchronized in a repository
@@ -34,8 +34,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
+      max-parallel: 5
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-eoan, ubuntu-focal, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, centos-7, centos-8, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-focal, fedora-27, fedora-31, debian-buster-i386]
         tox_packages_factor: [minimal-gcc_spkg, standard-gcc_spkg]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
@@ -99,6 +100,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
+      max-parallel: 1
       matrix:
         tox_system_factor: [conda-forge-ubuntu]
         tox_packages_factor: [minimal-gcc_spkg, standard-gcc_spkg]

.github/workflows/tox-optional.yml

@@ -36,7 +36,7 @@ jobs:
       fail-fast: false
       max-parallel: 6
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-eoan, ubuntu-focal, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, centos-7, centos-8, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-eoan, ubuntu-focal, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [maximal]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.github/workflows/tox.yml

@@ -36,7 +36,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-eoan, ubuntu-focal, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, centos-7, centos-8, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-eoan, ubuntu-focal, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.github/workflows/update-cygwin-yml.sh

@@ -1,2 +1,2 @@
 #!/usr/bin/env bash
-for X in standard-python2 minimal; do sed 's/\[standard\]/['$X']/g;s/CI cygwin-standard/CI cygwin-'$X'/g;' ci-cygwin-standard.yml > ci-cygwin-$X.yml; done
+for X in minimal; do sed 's/\[standard\]/['$X']/g;s/CI cygwin-standard/CI cygwin-'$X'/g;' ci-cygwin-standard.yml > ci-cygwin-$X.yml; done

.lgtm.yml

@@ -10,6 +10,7 @@ path_classifiers:
     - "**/species/library.py"
     - "**/categories/basic.py"
     - "**/combinat/ribbon.py"
+    - "**/combinat/family.py"
     - "**/interacts/geometry.py"
     - "**/matroids/advanced.py"
     - "**/matroids/named_matroids.py"

Makefile

@@ -35,7 +35,7 @@ sageruntime: base-toolchain
 
 # CONFIG_FILES lists all files that appear in AC_CONFIG_FILES in configure.ac;
 # except for build/make/Makefile-auto, which is unused by the build system
-CONFIG_FILES = build/make/Makefile src/Makefile src/bin/sage-env-config build/bin/sage-build-env-config build/pkgs/sage_conf/src/sage_conf.py build/pkgs/sage_conf/src/setup.cfg
+CONFIG_FILES = build/make/Makefile src/bin/sage-env-config build/bin/sage-build-env-config build/pkgs/sage_conf/src/sage_conf.py build/pkgs/sage_conf/src/setup.cfg
 
 # SPKG_COLLECT_FILES contains all files that influence the SAGE_SPKG_COLLECT macro
 SPKG_COLLECT_FILES = build/pkgs/*/type build/pkgs/*/package-version.txt build/pkgs/*/dependencies build/pkgs/*/requirements.txt build/pkgs/*/checksums.ini build/pkgs/*/spkg-install
@@ -49,7 +49,11 @@ build/make/Makefile: configure $(SPKG_COLLECT_FILES) $(CONFIG_FILES:%=%.in)
 	@if [ -x config.status ]; then \
 		./config.status --recheck && ./config.status; \
 	else \
-		./configure $$PREREQ_OPTIONS; \
+		echo >&2 '****************************************************************************'; \
+		echo >&2 'error: Sage source tree is unconfigured. Please run "./configure" first.'; \
+		echo >&2 'note:  Type "./configure --help" to see the available configuration options.'; \
+		echo >&2 '****************************************************************************'; \
+	        exit 1; \
 	fi
 
 # This is used to monitor progress towards Python 3 and prevent
@@ -106,14 +110,17 @@ bootstrap-clean:
 	rm -rf config configure build/make/Makefile-auto.in
 	rm -f src/doc/en/installation/*.txt
 	rm -rf src/doc/en/reference/spkg/*.rst
+	rm -f src/doc/en/reference/repl/*.txt
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean
 	rm -rf upstream
 
 # Remove everything that is not necessary to run Sage and pass all its
 # doctests.
-micro_release: sagelib-clean misc-clean
+micro_release:
+	$(MAKE) sagelib-clean
+	$(MAKE) misc-clean
 	@echo "Stripping binaries ..."
 	LC_ALL=C find local/lib local/bin -type f -exec strip '{}' ';' 2>&1 | grep -v "File format not recognized" |  grep -v "File truncated" || true
 	@echo "Removing sphinx artifacts..."

README.md

@@ -173,7 +173,7 @@ Guide](https://doc.sagemath.org/html/en/installation).
 
     - [Git] Alternatively, clone the Sage git repository:
 
-            $ git clone --branch master git://trac.sagemath.org/sage.git
+            $ git clone -c core.symlinks=true --branch master git://trac.sagemath.org/sage.git
 
       This will create the subdirectory `sage`.
 
@@ -183,12 +183,9 @@ 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 crucial that you use the Cygwin (or WSL)
-      version of `git`, and that you configure it as follows first:
-
-            $ git config --global core.autocrlf false
-            $ git config --global core.symlinks true
+      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`.
 
 3. `cd` into the source/build directory:
 
@@ -271,8 +268,8 @@ Guide](https://doc.sagemath.org/html/en/installation).
    guide](https://doc.sagemath.org/html/en/installation/source.html#environment-variables).
 
 11. Type `./configure`, followed by any options that you wish to use.
-   For example, to build a Python2-based Sage (which was the default
-   before Sage 9.0), use `./configure --with-python=2`.
+   For example, to build Sage with `gf2x` package supplied by Sage,
+   use `./configure --with-system-gf2x=no`.
 
    At the end of a successful `./configure` run, you may see messages
    recommending to install extra system packages using your package
@@ -422,13 +419,7 @@ through to another Makefile under `build/make/Makefile`.
 The latter `build/make/Makefile` *is* generated by an autoconf-generated
 `configure` script, using the template in `build/make/Makefile.in`.  This
 includes rules for building the Sage library itself (`make sagelib`), and for
-building and installing each of Sage's dependencies (e.g. `make python2`).
-
-Although it's possible to manually run Sage's `configure` script if one wants
-to provide some customizations (e.g. it is possible to select which BLAS
-implementation to use), the top-level `Makefile` will run `configure` for you,
-in order to build `build/make/Makefile` since it's a prerequisite for most of
-Sage's make targets.
+building and installing each of Sage's dependencies (e.g. `make gf2x`).
 
 The `configure` script itself, if it is not already built, can be generated by
 running the `bootstrap` script (the latter requires _GNU autotools_ being installed).
@@ -438,8 +429,9 @@ To summarize, running a command like `make python3` at the top-level of the
 source tree goes something like this:
 
 1. `make python3`
-2. run `./bootstrap` if `configure` does not exist
-3. run `./configure` if `build/make/Makefile` does not exist
+2. run `./bootstrap` if `configure` needs updating
+3. run `./configure` with any previously configured options if `build/make/Makefile`
+   needs updating
 4. `cd` into `build/make` and run the `install` script--this is little more
    than a front-end to running `make -f build/make/Makefile python3`, which
    sets some necessary environment variables and logs some information

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.2.beta1, Release Date: 2020-06-13
+SageMath version 9.2.beta5, Release Date: 2020-07-12

bootstrap

@@ -160,7 +160,7 @@ save () {
     # Create configure tarball
     echo "Creating $NEWCONFBALL..."
     mkdir -p upstream
-    tar zcf "$NEWCONFBALL" configure config/* build/make/Makefile-auto.in src/doc/en/installation/*.txt src/doc/en/reference/spkg/*.rst
+    tar zcf "$NEWCONFBALL" configure config/* build/make/Makefile-auto.in src/doc/en/installation/*.txt src/doc/en/reference/spkg/*.rst src/doc/en/reference/repl/*.txt
 
     # Update version
     echo "$NEWCONFVERSION" >$PKG/package-version.txt

build/bin/sage-logger

@@ -32,6 +32,7 @@ fi
 
 cmd="$1"
 logfile="$2"
+export SAGE_LOGFILE="$logfile"
 logname="$(basename $logfile .log)"
 logdir=`dirname "$logfile"`
 

build/bin/sage-print-system-package-command

@@ -58,6 +58,9 @@ case $system:$command in
     @(fedora*|redhat*|centos*):install)
         [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}yum install $system_packages"
         ;;
+    gentoo*:install)
+        [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}emerge $system_packages"
+        ;;
     arch*:install)
         [ -n "$system_packages" ] && echo "${PROMPT}${SUDO}pacman -S $system_packages"
         ;;