Merge tag '9.3.beta9' into t/30383/new_package_type__optional_enabled…

…_by_default

SageMath version 9.3.beta9, Release Date: 2021-03-14

.github/workflows/extract-sage-local.sh

@@ -1,26 +1,27 @@
 #!/usr/bin/env bash
 # to be run from $SAGE_ROOT, with arguments sage-local-${{ env.PREVIOUS_STAGES }}.tar
 
+if [ -z "$SAGE_LOCAL" ]; then
+    SAGE_LOCAL=$(pwd)/local
+fi
+
 # Show all tar files
 ls -l $*
 
 # We specifically use the cygwin tar so that symlinks are saved/restored correctly on Windows.
 for a in $*; do
     echo Extracting $a
-    tar xf $a
+    (cd / && tar xf -) < $a
     rm -f $a
 done
 
-# Also get rid of the stages that were not extracted
-rm -f sage-local-*.tar
-
 # We set the installation records to the same mtime so that no rebuilds due to dependencies
 # among these packages are triggered.
-(cd local/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
+(cd "$SAGE_LOCAL"/var/lib/sage/installed/ && touch .dummy && touch --reference=.dummy *)
 
 # Show what has been built already.
-ls -l local local/var/lib/sage/installed/
+ls -l "$SAGE_LOCAL" "$SAGE_LOCAL"/var/lib/sage/installed/
 df -h
 
 # Rebase!
-src/bin/sage-rebase.sh local
+src/bin/sage-rebase.sh "$SAGE_LOCAL"

.github/workflows/tox-experimental.yml

@@ -62,7 +62,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox-gcc_spkg.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -114,7 +114,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.

.github/workflows/tox-optional.yml

@@ -64,7 +64,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -107,7 +107,16 @@ jobs:
         os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, homebrew-macos-python3_xcode-gcc_spkg, conda-forge-macos]
         tox_packages_factor: [minimal, standard]
-        xcode_version_factor: [11.7, default, 12.3]
+        xcode_version_factor: [11.7, 12.2, default, 12.4]
+        include:
+          - 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_${{ matrix.xcode_version_factor }}
@@ -154,7 +163,7 @@ jobs:
       max-parallel: 1
       matrix:
         tox_system_factor: [conda-forge-ubuntu]
-        tox_packages_factor: [minimal, standard]
+        tox_packages_factor: [minimal, standard, environment, environment-optional]
     env:
       TOX_ENV: local-${{ 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 }}
@@ -163,7 +172,7 @@ jobs:
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
       - name: Build and test with tox
         # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
         # For doctesting, we use a lower parallelization to avoid timeouts.
@@ -196,7 +205,7 @@ jobs:
       - name: Install bootstrap prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(sed "s/#.*//;" build/pkgs/debian-bootstrap.txt)
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(build/bin/sage-get-system-packages debian _bootstrap)
       - name: Bootstrap with sage-update-version
         # We set SAGE_ROOT and SAGE_SRC by hand
         # because 'sage -sh' does not work with an unconfigured tree,
@@ -225,7 +234,7 @@ jobs:
         os: [ macos-10.15, macos-11.0 ]
         tox_system_factor: [macos-nobootstrap, macos-nobootstrap-python3_pythonorg]
         tox_packages_factor: [minimal]
-        xcode_version_factor: [default, 12]
+        xcode_version_factor: [11.7, 12.2, default, 12.4]
     env:
       TOX_ENV: local-${{ 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 }}-xcode_${{ matrix.xcode_version_factor }}

.gitignore

@@ -101,7 +101,7 @@ 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/graphs/graph_decompositions/sage_tdlib.cpp
 !src/sage/libs/eclib/wrap.cpp
 !src/sage/misc/inherit_comparison_impl.c
 !src/sage/modular/arithgroup/farey.cpp
@@ -118,6 +118,7 @@ src/sage/modular/arithgroup/farey_symbol.h
 !src/sage/stats/distributions/dgs_bern.c
 !src/sage/stats/distributions/dgs_gauss_dp.c
 !src/sage/stats/distributions/dgs_gauss_mp.c
+/src/cython_debug
 
 # Temporary build files
 build/temp.*/

.homebrew-build-env

@@ -23,7 +23,7 @@ export PKG_CONFIG_PATH
 LIBRARY_PATH="$HOMEBREW/lib$LIBRARY_PATH"
 [ -z "$CPATH" ] || CPATH=":${CPATH}"
 CPATH="$HOMEBREW/include$CPATH"
-for l in readline bzip2; do
+for l in readline bzip2 ntl; do
     if [ -d "$HOMEBREW/opt/$l/lib" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l/lib:$LIBRARY_PATH"
     fi

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.beta7", 
-    "version": "9.3.beta7", 
+    "title": "sagemath/sage: 9.3.beta9", 
+    "version": "9.3.beta9", 
     "upload_type": "software", 
-    "publication_date": "2021-02-07", 
+    "publication_date": "2021-03-14", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta7", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.3.beta9", 
             "relation": "isSupplementTo"
         }, 
         {

COPYING.txt

@@ -130,7 +130,6 @@ symmetrica                  MIT-like License (see below)
 sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
-termcap                     GPLv2+
 threejs                     MIT License
 tornado                     Apache License
 zlib                        Custom (Modified BSD)

README.md

@@ -219,9 +219,9 @@ Guide](https://doc.sagemath.org/html/en/installation).
    * Build tools: GNU `make`, GNU `m4`, `perl` (including
      ``ExtUtils::MakeMaker``), `ranlib`, `git`, `tar`, `bc`
 
-   * Any version of `python` (full installation including `urllib`),
-     but ideally version 3.7.x or 3.8.x, which will avoid having to build Sage's
-     own copy of Python 3.
+   * Python 3.4 or later, or Python 2.7, a full installation including
+     `urllib`; but ideally version 3.7.x, 3.8.x, or 3.9.x, which will
+     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),

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.beta7, Release Date: 2021-02-07
+SageMath version 9.3.beta9, Release Date: 2021-03-14

build/bin/sage-bootstrap-python

@@ -17,6 +17,9 @@ fi
 # So it needs to find a python that has the urllib module.
 # For example, on Debian buster, the python3-minimal package does NOT provide it.
 #
+# Also, Trac #20023 removed the vendored argparse library from sage_bootstrap,
+# so we test that python is new enough (>= 2.7) to run it.
+#
 # See https://trac.sagemath.org/ticket/29090
 
 # Trac #29890: Our first choice is "python", not "python3". This is to avoid
@@ -41,7 +44,7 @@ PYTHONS="python python3 python3.8 python3.7 python2.7 python3.6 python2"
 for PY in $PYTHONS; do
     PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
     if [ -n "$PYTHON" ]; then
-        if "$PYTHON" -c "import urllib; from hashlib import sha1; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
+        if "$PYTHON" -c "import argparse; import urllib; from hashlib import sha1; from os import listdir; listdir(\"$(pwd)\");" 2>/dev/null; then
             exec "$PYTHON" "$@"
         fi
     fi

build/bin/sage-build-env

@@ -24,34 +24,34 @@
 # The compiler flags are set in order of priority by
 # 1) environment variables
 # 2) flags set at configuration time
-if [ "x$CFLAGS" == "x" ]; then
+if [ "x$CFLAGS" = "x" ]; then
     export ORIGINAL_CFLAGS="$CONFIGURED_CFLAGS"
 else
     export ORIGINAL_CFLAGS="$CFLAGS"
 fi
-if [ "x$CXXFLAGS" == "x" ]; then
+if [ "x$CXXFLAGS" = "x" ]; then
     export ORIGINAL_CXXFLAGS="$CONFIGURED_CXXFLAGS"
 else
     export ORIGINAL_CXXFLAGS="$CXXFLAGS"
 fi
-if [ "x$FCFLAGS" == "x" ]; then
+if [ "x$FCFLAGS" = "x" ]; then
     export ORIGINAL_FCFLAGS="$CONFIGURED_FCFLAGS"
 else
     export ORIGINAL_FCFLAGS="$FCFLAGS"
 fi
-if [ "x$F77FLAGS" == "x" ]; then
+if [ "x$F77FLAGS" = "x" ]; then
     export ORIGINAL_F77FLAGS="$CONFIGURED_F77FLAGS"
 else
     export ORIGINAL_F77FLAGS="$F77FLAGS"
 fi
 
 # We optimize according to $SAGE_DEBUG.
-if [ "x$ORIGINAL_CFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_CFLAGS" = "x" ]; then
     # Evaluate SAGE_DEBUG:
-    if [ "x$SAGE_DEBUG" == "xyes" ]; then
+    if [ "x$SAGE_DEBUG" = "xyes" ]; then
         export CFLAGS_NON_NATIVE="-Og -g"
         export CFLAGS_O3_NON_NATIVE="-Og -g"
-    elif [ "x$SAGE_DEBUG" == "xno" ]; then
+    elif [ "x$SAGE_DEBUG" = "xno" ]; then
         export CFLAGS_NON_NATIVE="-O2"
         export CFLAGS_O3_NON_NATIVE="-O3"
     else
@@ -69,7 +69,7 @@ else
 fi
 
 # Copy to CXXFLAGS if this is not set.
-if [ "x$ORIGINAL_CXXFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_CXXFLAGS" = "x" ]; then
     export CXXFLAGS="$CFLAGS"
     export CXXFLAGS_O3="$CFLAGS_O3"
     export CXXFLAGS_NON_NATIVE="$CFLAGS_NON_NATIVE"
@@ -82,7 +82,7 @@ else
 fi
 
 # Copy CFLAGS to FCFLAGS if this is not set.
-if [ "x$ORIGINAL_FCFLAGS" == "x" ]; then
+if [ "x$ORIGINAL_FCFLAGS" = "x" ]; then
     export FCFLAGS="$CFLAGS"
     export FCFLAGS_O3="$CFLAGS_O3"
     export FCFLAGS_NON_NATIVE="$CFLAGS_NON_NATIVE"
@@ -95,7 +95,7 @@ else
 fi
 
 # Copy FCFLAGS to F77FLAGS if this is not set.
-if [ "x$ORIGINAL_F77FLAGS" == "x" ]; then
+if [ "x$ORIGINAL_F77FLAGS" = "x" ]; then
     export F77FLAGS="$FCFLAGS"
     export F77FLAGS_O3="$FCFLAGS_O3"
     export F77FLAGS_NON_NATIVE="$FCFLAGS_NON_NATIVE"

build/bin/sage-build-env-config.in

@@ -27,7 +27,7 @@ export SAGE_FAT_BINARY="@SAGE_FAT_BINARY@"
 
 # Export SAGE_DEBUG if this was enabled during configure,
 # but be respectful of the current settings.
-if [ "x$SAGE_DEBUG" == "x" ]; then
+if [ "x$SAGE_DEBUG" = "x" ]; then
     export SAGE_DEBUG="@SAGE_DEBUG@"
 fi
 
@@ -106,3 +106,5 @@ export SAGE_FREETYPE_PREFIX="@SAGE_FREETYPE_PREFIX@"
 export SAGE_SUITESPARSE_PREFIX="@SAGE_SUITESPARSE_PREFIX@"
 
 export SAGE_CONFIGURE_FFLAS_FFPACK="@SAGE_CONFIGURE_FFLAS_FFPACK@"
+
+export SAGE_EDITABLE="@SAGE_EDITABLE@"

build/bin/sage-dist-helpers

@@ -227,17 +227,14 @@ sdh_pip_install() {
     sdh_store_and_pip_install_wheel .
 }
 
-sdh_store_and_pip_install_wheel() {
+sdh_store_wheel() {
     if [ -n "$SAGE_DESTDIR" ]; then
         local sudo=""
-        # --no-warn-script-location: Suppress a warning caused by --root
-        local root="--root=$SAGE_DESTDIR --no-warn-script-location"
     else
         local sudo="$SAGE_SUDO"
-        local root=""
     fi
     if [ "$*" != "." ]; then
-        sdh_die "Error: sdh_store_and_pip_install_wheel requires . as only argument"
+        sdh_die "Error: sdh_store_wheel requires . as only argument"
     fi
     wheel=""
     for w in dist/*.whl; do
@@ -252,11 +249,24 @@ sdh_store_and_pip_install_wheel() {
         sdh_die "Error: no wheel found after building"
     fi
 
-    $sudo sage-pip-install $root "$wheel" || \
-        sdh_die "Error installing $wheel"
     mkdir -p "${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}" && \
         $sudo mv "$wheel" "${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}/" || \
         sdh_die "Error storing $wheel"
+    wheel="${SAGE_DESTDIR}${SAGE_SPKG_WHEELS}/${wheel##*/}"
+}
+
+sdh_store_and_pip_install_wheel() {
+    sdh_store_wheel "$@"
+    if [ -n "$SAGE_DESTDIR" ]; then
+        local sudo=""
+        # --no-warn-script-location: Suppress a warning caused by --root
+        local root="--root=$SAGE_DESTDIR --no-warn-script-location"
+    else
+        local sudo="$SAGE_SUDO"
+        local root=""
+    fi
+    $sudo sage-pip-install $root "$wheel" || \
+        sdh_die "Error installing ${wheel##*/}"
 }
 
 sdh_cmake() {