Merge tag '9.2.beta6' into t/29441/public/29441

SageMath version 9.2.beta6, Release Date: 2020-07-25
sagemath · Jul 25, 2020 · 54d0f99 · 54d0f99
2 parents 314b15f + ddaba54
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diff --git a/.github/workflows/tox-experimental.yml b/.github/workflows/tox-experimental.yml
@@ -0,0 +1,144 @@
+name: Test experimental packages with tox
+
+## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with select environments,
+## whenever a GitHub pull request is opened or synchronized in a repository
+## where GitHub Actions are enabled.
+##
+## It builds and checks some sage spkgs as defined in TARGETS.
+##
+## A job succeeds if there is no error.
+##
+## The build is run with "make V=0", so the build logs of individual packages are suppressed.
+##
+## At the end, all package build logs that contain an error are printed out.
+##
+## After all jobs have finished (or are canceled) and a short delay,
+## tar files of all logs are made available as "build artifacts".
+
+#on: [push, pull_request]
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+  push:
+    tags:
+      - '*'
+
+env:
+  TARGETS_PRE: build/make/Makefile
+  TARGETS:     build/make/Makefile
+  # TARGETS_OPTIONAL see below
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    strategy:
+      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, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
+        tox_packages_factor: [maximal]
+        targets_pattern: [0-g, h-o, p, q-z]
+    env:
+      TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
+      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
+      DOCKER_TARGETS: configured with-targets with-targets-optional
+      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :experimental: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep '^[${{ matrix.targets_pattern }}]' ) )"
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 500
+      - name: fetch tags
+        run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+      - name: free disk space
+        run: |
+          sudo swapoff -a
+          sudo rm -f /swapfile
+          sudo apt clean
+          docker rmi $(docker image ls -aq)
+          df -h
+      - name: Install test prerequisites
+        run: |
+          sudo DEBIAN_FRONTEND=noninteractive apt-get update
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install python-tox
+      - run: |
+          set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"
+      - name: Copy logs from the docker image or build container
+        run: |
+          mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"
+          cp -r .tox/$TOX_ENV/Dockerfile .tox/$TOX_ENV/log "artifacts/$LOGS_ARTIFACT_NAME"
+          if [ -f .tox/$TOX_ENV/Dockertags ]; then CONTAINERS=$(docker create $(tail -1 .tox/$TOX_ENV/Dockertags) /bin/bash || true); fi
+          if [ -n "$CONTAINERS" ]; then for CONTAINER in $CONTAINERS; do for ARTIFACT in /sage/logs; do docker cp $CONTAINER:$ARTIFACT artifacts/$LOGS_ARTIFACT_NAME && HAVE_LOG=1; done; if [ -n "$HAVE_LOG" ]; then break; fi; done; fi
+        if: always()
+      - uses: actions/upload-artifact@v1
+        with:
+          path: artifacts
+          name: ${{ env.LOGS_ARTIFACT_NAME }}
+        if: always()
+      - name: Print out logs for immediate inspection
+        # and markup the output with GitHub Actions logging commands
+        run: |
+          .github/workflows/scan-logs.sh "artifacts/$LOGS_ARTIFACT_NAME"
+        if: always()
+      - name: Push docker images
+        run: |
+          if [ -f .tox/$TOX_ENV/Dockertags ]; then
+            TOKEN="${{ secrets.DOCKER_PKG_GITHUB_TOKEN }}"
+            if [ -z "$TOKEN" ]; then
+              TOKEN="${{ secrets.GITHUB_TOKEN }}"
+            fi
+            echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+            for a in $(cat .tox/$TOX_ENV/Dockertags); do
+              FULL_TAG=docker.pkg.github.com/${{ github.repository }}/$a
+              docker tag $a $FULL_TAG
+              echo Pushing $FULL_TAG
+              docker push $FULL_TAG
+            done || echo "(Ignoring errors)"
+          fi
+        if: always()
+
+  local-macos:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, conda-forge-macos]
+        tox_packages_factor: [maximal]
+        targets_pattern: [0-g, h-o, p, q-z]
+    env:
+      TOX_ENV: local-${{ 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 }}
+      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :experimental: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep '^[${{ matrix.targets_pattern }}]' ) )"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install test prerequisites
+        run: |
+          brew 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.
+        run: |
+          curl -o python3.pkg https://www.python.org/ftp/python/3.7.7/python-3.7.7-macosx10.9.pkg
+          sudo installer -verbose -pkg python3.pkg -target /
+        if: contains(matrix.tox_system_factor, 'python3_pythonorg')
+      - 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.
+        run: |
+          MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS
+      - name: Prepare logs artifact
+        run: |
+          mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"
+        if: always()
+      - uses: actions/upload-artifact@v1
+        with:
+          path: artifacts
+          name: ${{ env.LOGS_ARTIFACT_NAME }}
+        if: always()
+      - name: Print out logs for immediate inspection
+        # and markup the output with GitHub Actions logging commands
+        run: |
+          .github/workflows/scan-logs.sh "artifacts/$LOGS_ARTIFACT_NAME"
+        if: always()
diff --git a/.github/workflows/tox-optional.yml b/.github/workflows/tox-optional.yml
@@ -1,4 +1,4 @@
-name: Run SAGE_ROOT/tox.ini TARGETS_OPTIONAL
+name: Test optional packages with tox
 
 ## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with select environments,
 ## whenever a GitHub pull request is opened or synchronized in a repository
@@ -27,7 +27,7 @@ on:
 env:
   TARGETS_PRE: build/make/Makefile
   TARGETS:     build/make/Makefile
-  TARGETS_OPTIONAL: 4ti2 pynormaliz qepcad lrslib latte_int topcom barvinok isl qhull sage_numerical_backends_coin primecount plantri polymake jupymake kenzo libsemigroups mcqd meataxe mpfrcx openssl p_group_cohomology rst2ipynb sirocco tdlib tides
+  # TARGETS_OPTIONAL see below
 
 jobs:
   docker:
@@ -38,10 +38,14 @@ jobs:
       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, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-eoan-i386, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [maximal]
+        targets_pattern: [0-g, h-o, p, q-z]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       DOCKER_TARGETS: configured with-targets with-targets-optional
+      # Test all optional packages, but do not test huge packages,
+      # and do not test packages that require external software
+      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :optional: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
         with:
@@ -104,9 +108,13 @@ jobs:
       matrix:
         tox_system_factor: [homebrew-macos, homebrew-macos-python3_xcode, homebrew-macos-python3_xcode-nokegonly, homebrew-macos-python3_pythonorg, conda-forge-macos]
         tox_packages_factor: [maximal]
+        targets_pattern: [0-g, h-o, p, q-z]
     env:
       TOX_ENV: local-${{ 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 }}
+      # Test all optional packages, but do not test huge packages
+      # and do not test packages that require external software
+      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :optional: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
       - name: Install test prerequisites

diff --git a/README.md b/README.md
@@ -255,11 +255,6 @@ Guide](https://doc.sagemath.org/html/en/installation).
    powerful machines, you might even consider `-j16`, as building with
    more jobs than CPU cores can speed things up further.
 
-   If you want to run the test suite for each individual Sage package
-   as it gets installed, type `export SAGE_CHECK="yes"`. This will run
-   each test suite, raising an error if any failure occurs.  If set to
-   ``warn``, then only a warning is printed in this case.
-
    To reduce the terminal output during the build, type `export V=0`.
    (`V` stands for "verbosity".)
 

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 9.2.beta5, Release Date: 2020-07-12
+SageMath version 9.2.beta6, Release Date: 2020-07-25
diff --git a/bootstrap b/bootstrap
@@ -206,6 +206,7 @@ mkdir config 2>/dev/null
 # Get autotools from our own package into PATH (Trac #21214).
 # If Sage has not been built yet, this will fail due to a missing
 # sage-env-config. We just ignore that error.
+source src/bin/sage-env-config 2>/dev/null
 source src/bin/sage-env 2>/dev/null
 
 

diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
@@ -166,6 +166,7 @@ fi
 # The following sets environment variables for building packages.
 # Since this is sourced, it returns a non-zero value on errors rather
 # than exiting.  Using dot suggested by W. Cheung.
+. sage-env-config
 . sage-env
 
 
@@ -488,7 +489,7 @@ export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"
 export PKG_VER="$PKG_VER"
 
-for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env" "\$SAGE_ROOT/build/bin/sage-build-env-config"; do
+for lib in "\$SAGE_ROOT/build/bin/sage-dist-helpers" "\$SAGE_SRC/bin/sage-env-config" "\$SAGE_SRC/bin/sage-env" "\$SAGE_ROOT/build/bin/sage-build-env-config"; do
     source "\$lib"
     if [ \$? -ne 0 ]; then
         echo >&2 "Error: failed to source \$lib"

diff --git a/build/bin/write-dockerfile.sh b/build/bin/write-dockerfile.sh
@@ -43,6 +43,11 @@ case $SYSTEM in
 ARG BASE_IMAGE=ubuntu:latest
 FROM \${BASE_IMAGE} as with-system-packages
 EOF
+        if [ -n "$DIST_UPGRADE" ]; then
+            cat <<EOF
+RUN sed -i.bak $DIST_UPGRADE /etc/apt/sources.list && apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y dist-upgrade
+EOF
+        fi
         EXISTS="2>/dev/null >/dev/null apt-cache show"
         UPDATE="apt-get update &&"
         INSTALL="DEBIAN_FRONTEND=noninteractive apt-get install -qqq --no-install-recommends --yes"

diff --git a/build/make/Makefile.in b/build/make/Makefile.in
@@ -517,13 +517,15 @@ endif
 #
 # $(INST)/<pkgname>-<pkgvers>: <dependencies>
 #     $(AM_V_at)cd '$SAGE_ROOT' && \\
+#         . '$SAGE_ROOT/src/bin/sage-env-config' && \\
 #         . '$SAGE_ROOT/src/bin/sage-env' && \\
 #         sage-logger -p '$SAGE_ROOT/build/pkgs/<pkgname>/spkg-install' '$(SAGE_LOGS)/<pkgname>.log'
 #
 # <pkgname>: $(INST)/<pkgname>-<pkgvers>
 #
 # <pkgname>-clean:
 #     -$(AM_V_at)cd '$SAGE_ROOT' && \\
+#         . '$SAGE_ROOT/src/bin/sage-env-config' && \\
 #         . '$SAGE_ROOT/src/bin/sage-env' && \\
 #         '$SAGE_ROOT/build/pkgs/$PKG_NAME/spkg-uninstall'
 
@@ -536,15 +538,19 @@ $(1)-build-deps: $(3)
 
 $$(INST)/$(1)-$(2): $(3)
 	$(AM_V_at)cd '$$(SAGE_ROOT)/build/pkgs/$(1)' && \
-		. '$$(SAGE_ROOT)/src/bin/sage-env' && . '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		. '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log'
 	touch "$$@"
 
 $(1): $$(INST)/$(1)-$(2)
 
 $(1)-uninstall:
 	-$(AM_V_at)cd '$$(SAGE_ROOT)/build/pkgs/$(1)' && \
-		. '$$(SAGE_ROOT)/src/bin/sage-env' && . '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env-config' && \
+		. '$$(SAGE_ROOT)/src/bin/sage-env' && \
+		. '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-uninstall'
 	-rm -f "$$(INST)/$(1)-$(2)"
 

diff --git a/build/pkgs/cmake/spkg-check.in b/build/pkgs/cmake/spkg-check.in
@@ -1,24 +1,8 @@
-if [ "$UNAME" = Darwin ]; then
-    CC=clang
-    CXX=clang++
-fi
-
-cd src
-unset MACOSX_DEPLOYMENT_TARGET
-# Supress tests failing for reason out of our controls
-FAILING_TESTS="CTestTestStopTime|TestUpload|ctest_submit"
-# gui interface may pull dependency conflicting with
-# sage libraries
-# (1) QT libraries
-FAILING_TESTS="${FAILING_TESTS}|Qt5Autogen|Qt4Autogen|Qt4Targets|Qt4And5AutomocReverse"
-# (2) GTK2
-FAILING_TESTS="${FAILING_TESTS}|GTK2Components|GTK2Targets"
-# BundleUtilities test is failing on some platforms, skipped in Gentoo for that reason
-FAILING_TESTS="${FAILING_TESTS}|BundleUtilities"
-# Test failing on freeBSD. Upstream acknoledged the test is faulty
-# on that platform https://gitlab.kitware.com/cmake/cmake/issues/16887
-if [ "$UNAME" = "FreeBSD" ]; then
-    FAILING_TESTS="${FAILING_TESTS}|RunCMake.GNUInstallDirs"
-fi
-ctest --extra-verbose --output-on-failure -E "(${FAILING_TESTS})"
+# Do not run a test suite: see https://trac.sagemath.org/ticket/30093.
+#
+# - The test suite takes a long time and can fail in minor ways.
+# - If some major aspect of cmake fails, it only affects the build
+#   process of Sage, not the mathematical correctness of its results.
+# - If some minor aspect of cmake fails, it won't affect anything about Sage.
 
+echo "We skip the test suite for cmake: see https://trac.sagemath.org/ticket/30093."
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1af52fa76e46ec00e41627bf8c3b2d4ac440968e
-md5=426664a892601af3cf54cd33648486a7
-cksum=1836178061
+sha1=eac827f97c1258cf6524a81084172a43bf7c4680
+md5=bf07fb027bc4c586edf10132298fa363
+cksum=546608769
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-339b4599590f3dc3acec5eace4b7a82f210d3219
+e41d396f5d30996ae515399b28675a60e97a1996
diff --git a/build/pkgs/curl/spkg-check.in b/build/pkgs/curl/spkg-check.in
@@ -1,2 +1,8 @@
-cd src
-$MAKE check
+# Do not run a test suite: see https://trac.sagemath.org/ticket/30093.
+#
+# - The test suite takes a long time and can fail in minor ways.
+# - If some major aspect of curl fails, it only affects the build
+#   process of Sage, not the mathematical correctness of its results.
+# - If some minor aspect of curl fails, it won't affect anything about Sage.
+
+echo "We skip the test suite for curl: see https://trac.sagemath.org/ticket/30093."
diff --git a/build/pkgs/cython/checksums.ini b/build/pkgs/cython/checksums.ini
@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=02278e5a972ffc4856451f507903db68d08cfd6e
-md5=0936311ccd09f1164ab2f46ca5cd8c3b
-cksum=1144843552
+sha1=3aafce4489a7bc7a48c843cdfb8dac4677fdac50
+md5=12c5e45af71dcc6dff28cdcbcbef6f39
+cksum=3658613797
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz
diff --git a/build/pkgs/cython/package-version.txt b/build/pkgs/cython/package-version.txt
@@ -1 +1 @@
-0.29.17
+0.29.21
diff --git a/build/pkgs/ecl/package-version.txt b/build/pkgs/ecl/package-version.txt
@@ -1 +1 @@
-20.4.24.p0
+20.4.24.p1
diff --git a/build/pkgs/ecl/patches/0001-unicode-fix-ecl_string_case-for-non-ascii-characters.patch b/build/pkgs/ecl/patches/0001-unicode-fix-ecl_string_case-for-non-ascii-characters.patch
@@ -0,0 +1,47 @@
+From 29239fa1b38f55b9a263b9582a43bae18cb5980d Mon Sep 17 00:00:00 2001
+From: Marius Gerbershagen <marius.gerbershagen@gmail.com>
+Date: Wed, 6 May 2020 20:58:20 +0200
+Subject: [PATCH 1/3] unicode: fix ecl_string_case for non-ascii characters
+
+Problem reported and fix provided by Vladimir Sedach on the ecl-devel
+mailing list.
+---
+ src/c/character.d | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/src/c/character.d b/src/c/character.d
+index a69b6e4b..c3ef328a 100644
+--- a/src/c/character.d
++++ b/src/c/character.d
+@@ -99,6 +99,7 @@ cl_both_case_p(cl_object c)
+ int
+ ecl_string_case(cl_object s)
+ {
++  /* Returns 1 if string is all uppercase, -1 if all lowercase, and 0 if mixed case */
+   int upcase;
+   cl_index i;
+   ecl_base_char *text;
+@@ -106,16 +107,16 @@ ecl_string_case(cl_object s)
+   switch (ecl_t_of(s)) {
+ #ifdef ECL_UNICODE
+   case t_string:
+-    s = si_coerce_to_base_string(s);
+ #endif
+   case t_base_string:
+-    text = (ecl_base_char*)s->base_string.self;
+     for (i = 0, upcase = 0; i < s->base_string.dim; i++) {
+-      if (ecl_upper_case_p(text[i])) {
++      ecl_character c = ecl_char(s, i);
++
++      if (ecl_upper_case_p(c)) {
+         if (upcase < 0)
+           return 0;
+         upcase = +1;
+-      } else if (ecl_lower_case_p(text[i])) {
++      } else if (ecl_lower_case_p(c)) {
+         if (upcase > 0)
+           return 0;
+         upcase = -1;
+-- 
+2.26.2
+