Merge branch 'develop' into fix_quaternion_37488

vbraun · Mar 29, 2024 · 949d94e · 949d94e
2 parents 54a1376 + b693ea9
commit 949d94e
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diff --git a/.ci/merge-fixes.sh b/.ci/merge-fixes.sh
@@ -42,6 +42,7 @@ for REPO in ${SAGE_CI_FIXES_FROM_REPOSITORIES:-sagemath/sage}; do
                     # Considered alternative: Use https://github.com/$REPO/pull/$a.diff,
                     # which squashes everything into one diff without commit metadata.
                     PULL_URL="https://github.com/$REPO/pull/$a"
+                    PULL_SHORT="$REPO#$a"
                     PULL_FILE="$REPO_FILE-$a"
                     PATH=build/bin:$PATH build/bin/sage-download-file --quiet "$PULL_URL.patch" $PULL_FILE.patch
                     date -u +"%Y-%m-%dT%H:%M:%SZ" > $PULL_FILE.date  # Record the date, for future reference
@@ -67,7 +68,7 @@ for REPO in ${SAGE_CI_FIXES_FROM_REPOSITORIES:-sagemath/sage}; do
                         git am --signoff --show-current-patch=diff
                         echo "--------------------------------------------------------------------8<-----------------------------"
                         echo "::endgroup::"
-                        echo "Failure applying $PULL_URL as a patch, resetting"
+                        echo "Failure applying $PULL_SHORT as a patch, resetting"
                         git am --signoff --abort
                     fi
                 done

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -35,13 +35,13 @@ jobs:
         uses: actions/checkout@v4
       - name: Merge CI fixes from sagemath/sage
         run: |
-          .ci/merge-fixes.sh
+          mkdir -p upstream
+          .ci/merge-fixes.sh 2>&1 | tee upstream/ci_fixes.log
         env:
           GH_TOKEN: ${{ github.token }}
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
       - name: Store CI fixes in upstream artifact
         run: |
-          mkdir -p upstream
           if git format-patch --stdout test_base > ci_fixes.patch; then
             cp ci_fixes.patch upstream/
           fi

diff --git a/.github/workflows/ci-linux.yml b/.github/workflows/ci-linux.yml
@@ -39,6 +39,7 @@ jobs:
     uses: ./.github/workflows/docker.yml
     with:
       # Build from scratch
+      free_disk_space: true
       docker_targets: "with-system-packages configured with-targets-pre with-targets"
       # FIXME: duplicated from env.TARGETS
       targets_pre: all-sage-local

diff --git a/.github/workflows/ci-macos.yml b/.github/workflows/ci-macos.yml
@@ -34,6 +34,7 @@ jobs:
     uses: ./.github/workflows/macos.yml
     with:
       stage: "1"
+      timeout: 14400
 
   stage-2:
     uses: ./.github/workflows/macos.yml
@@ -90,7 +91,7 @@ jobs:
         run: |
           git config --global user.email "nobody@example.com"
           git config --global user.name "Sage GitHub CI"
-          SAGE_ROOT=. SAGE_SRC=./src src/bin/sage-update-version $(git describe --tags) || echo "(ignoring error)"
+          SAGE_ROOT=. SAGE_SRC=./src src/bin/sage-update-version $(cat src/VERSION.txt).dev0 || echo "(ignoring error)"
       - name: make dist
         run: |
           ./configure --enable-download-from-upstream-url && make dist
@@ -108,7 +109,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        os: [ macos-11, macos-12 ]
+        os: [ macos-11, macos-12, macos-14 ]
         tox_system_factor: [macos-nobootstrap]
         tox_packages_factor: [minimal]
         xcode_version_factor: [default]
@@ -129,7 +130,7 @@ 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 sudo mv $a $a-moved; done)
+          (cd $(brew --prefix) && 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
@@ -140,7 +141,8 @@ jobs:
         # 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
+          (sleep 20000; pkill make) &
+          MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=6 $TARGETS
       - name: Prepare logs artifact
         run: |
           mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"

diff --git a/.github/workflows/doc-build-pdf.yml b/.github/workflows/doc-build-pdf.yml
@@ -29,13 +29,13 @@ jobs:
         uses: actions/checkout@v4
       - name: Merge CI fixes from sagemath/sage
         run: |
-          .ci/merge-fixes.sh
+          mkdir -p upstream
+          .ci/merge-fixes.sh 2>&1 | tee upstream/ci_fixes.log
         env:
           GH_TOKEN: ${{ github.token }}
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
       - name: Store CI fixes in upstream artifact
         run: |
-          mkdir -p upstream
           if git format-patch --stdout test_base > ci_fixes.patch; then
             cp ci_fixes.patch upstream/
           fi

diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml
@@ -24,13 +24,13 @@ jobs:
         uses: actions/checkout@v4
       - name: Merge CI fixes from sagemath/sage
         run: |
-          .ci/merge-fixes.sh
+          mkdir -p upstream
+          .ci/merge-fixes.sh 2>&1 | tee upstream/ci_fixes.log
         env:
           GH_TOKEN: ${{ github.token }}
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
       - name: Store CI fixes in upstream artifact
         run: |
-          mkdir -p upstream
           if git format-patch --stdout test_base > ci_fixes.patch; then
             cp ci_fixes.patch upstream/
           fi

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -248,9 +248,8 @@ jobs:
       - 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
+          cp -r .tox/$TOX_ENV/* "artifacts/$LOGS_ARTIFACT_NAME"
+          rm -rf "artifacts/$LOGS_ARTIFACT_NAME"/{bin,lib,pyvenv.cfg}
         if: always()
       - uses: actions/upload-artifact@v3
         with:
@@ -262,9 +261,46 @@ jobs:
         run: |
           .github/workflows/scan-logs.sh "artifacts/$LOGS_ARTIFACT_NAME"
         if: always()
-      - name: List docker images
+      - name: List Docker images
         run: |
-          if [ -f .tox/$TOX_ENV/Dockertags ]; then
-             cat .tox/$TOX_ENV/Dockertags
+          if [ -n "$DOCKER_PUSH_REPOSITORY" -a -f .tox/$TOX_ENV/Dockertags.pushed ]; then
+             set -- $(cat .tox/$TOX_ENV/Dockertags.pushed)
+             case $# in
+                 1) images="image";  one_image="the image";;
+                 *) images="images"; one_image="one of the images";;
+             esac
+             echo "::notice title=Docker $images pushed::Pushed $images $*)"
+             echo
+             echo "To pull $one_image and enter the container, type:"
+             echo
+             for TAG in $*; do
+                 echo "  \$ docker run -it $TAG bash"
+             done
+             echo
+             echo "To use $one_image as the base for an incremental build, type:"
+             echo
+             TOX_ENV_SANS_INCREMENTAL=${TOX_ENV/-incremental/}
+             DOCKER_IMAGE=${TOX_ENV_SANS_INCREMENTAL#docker-}
+             for TAG in $*; do
+                 echo -n "  \$"
+                 if [ "$DOCKER_PUSH_REPOSITORY" != "ghcr.io/sagemath/sage/" ]; then
+                     echo -n " FROM_DOCKER_REPOSITORY=$DOCKER_PUSH_REPOSITORY"
+                 fi
+                 eval DOCKER_TARGET=\${TAG#*$DOCKER_IMAGE-}
+                 DOCKER_TARGET=${DOCKER_TARGET%:*}
+                 if [ "$DOCKER_TARGET" != "with-targets" ]; then
+                     echo -n " FROM_DOCKER_TARGET=$DOCKER_TARGET"
+                 fi
+                 echo " FROM_DOCKER_TAG=${TAG#*:} tox -e $TOX_ENV_SANS_INCREMENTAL-incremental"
+             done
+          elif [ -n "$DOCKER_PUSH_REPOSITORY" -a -f .tox/$TOX_ENV/Dockertags ]; then
+             echo "Unable to push Docker images to $DOCKER_PUSH_REPOSITORY."
+             echo "This is normal in a pull request to sagemath/sage or to another user's repository."
+             echo
+             echo "If you need Docker images, "
+             echo " - either run this GitHub Actions workflow in your repository fork"
+             echo " - or use the method described in https://doc.sagemath.org/html/en/developer/portability_testing.html#automatic-docker-based-build-testing-using-tox"
+          else
+             echo "No Docker images created."
           fi
-        if: always()
+        if: always() && ${{ inputs.docker_push_repository }}
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -19,17 +19,21 @@ on:
         type: string
       # System configuration
       osversion_xcodeversion_toxenv_tuples:
+        # As of 2024-02, "runs-on: macos-latest" is macos-12.
+        # and "runs-on: macos-14" selects the new M1 runners.
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
         description: 'Stringified JSON object'
         default: >-
-          [["latest", "",             "homebrew-macos-usrlocal-minimal"],
-           ["latest", "",             "homebrew-macos-usrlocal-standard"],
-           ["11",     "xcode_13.2.1", "homebrew-macos-usrlocal-minimal"],
+          [["11",     "xcode_13.2.1", "homebrew-macos-usrlocal-minimal"],
+           ["12",     "",             "homebrew-macos-usrlocal-minimal"],
            ["12",     "",             "homebrew-macos-usrlocal-standard"],
+           ["12",     "",             "homebrew-macos-usrlocal-python3_xcode-standard"],
+           ["12",     "",             "homebrew-macos-usrlocal-maximal"],
            ["13",     "xcode_15.0",   "homebrew-macos-usrlocal-standard"],
-           ["latest", "",             "homebrew-macos-usrlocal-maximal"],
-           ["latest", "",             "homebrew-macos-usrlocal-python3_xcode-standard"],
+           ["14",     "",             "homebrew-macos-opthomebrew-standard"],
            ["latest", "",             "conda-forge-macos-minimal"],
-           ["latest", "",             "conda-forge-macos-standard"]]
+           ["latest", "",             "conda-forge-macos-standard"],
+           ["14",     "",             "conda-forge-macos-standard"]]
         type: string
       extra_sage_packages:
         description: 'Extra Sage packages to install as system packages'
@@ -41,6 +45,10 @@ on:
       free_disk_space:
         default: false
         type: boolean
+      timeout:
+        description: 'Elapsed time (seconds) at which to kill the build'
+        default: 20000
+        type: number
       #
       # For use in upstream CIs.
       #
@@ -74,10 +82,16 @@ jobs:
           repository: ${{ inputs.sage_repo }}
           ref: ${{ inputs.sage_ref }}
           fetch-depth: 10000
-
+      - uses: actions/setup-python@v5
+        # As of 2024-02-03, the macOS M1 runners do not have preinstalled python or pipx.
+        # Installing pipx follows the approach of https://github.com/pypa/cibuildwheel/pull/1743
+        id: python
+        with:
+          python-version: "3.8 - 3.12"
+          update-environment: false
       - name: Install test prerequisites
         run: |
-          brew install tox
+          "${{ steps.python.outputs.python-path }}" -m pip install pipx
       - name: Download upstream artifact
         uses: actions/download-artifact@v3
         with:
@@ -129,7 +143,8 @@ jobs:
             *)               export TARGETS_PRE="${{ inputs.targets_pre }}" TARGETS="${{ inputs.targets }} TARGETS_OPTIONAL="${{ inputs.targets_optional }}
                              ;;
           esac
-          MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS
+          (sleep ${{ inputs.timeout }}; pkill make) &
+          MAKE="make -j12" EXTRA_SAGE_PACKAGES="${{ inputs.extra_sage_packages }}" "${{ steps.python.outputs.python-path }}" -m pipx run tox -e $TOX_ENV -- SAGE_NUM_THREADS=6 $TARGETS
       - name: Prepare logs artifact
         run: |
           mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"

diff --git a/.upstream.d/20-git.luolix.top-sagemath-sage-releases b/.upstream.d/20-git.luolix.top-sagemath-sage-releases
@@ -1,5 +1,5 @@
 # Upstream packages as uploaded as GitHub release assets.
 # This file is automatically updated by the sage-update-version script.
+https://github.com/sagemath/sage/releases/download/10.4/
 https://github.com/sagemath/sage/releases/download/10.3/
 https://github.com/sagemath/sage/releases/download/10.2/
-https://github.com/sagemath/sage/releases/download/10.1/
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.3.rc0
+version: 10.4.beta0
 doi: 10.5281/zenodo.593563
-date-released: 2024-02-25
+date-released: 2024-03-25
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -37,6 +37,4 @@ Sage can more effectively collaborate with others if they follow this code.
 
 If you believe someone is violating the code of conduct, we ask that you report
 it to https://groups.google.com/g/sage-abuse. The group administrators will
-consider the issue and explore resolutions. It is also possible to move heated
-discussions to https://groups.google.com/g/sage-flame.
-
+consider the issue and explore resolutions.
diff --git a/Makefile b/Makefile
@@ -44,13 +44,25 @@ SAGE_ROOT_LOGS = logs
 # except for build/make/Makefile-auto, which is unused by the build system
 CONFIG_FILES = build/make/Makefile src/bin/sage-env-config build/bin/sage-build-env-config pkgs/sage-conf/_sage_conf/_conf.py
 
-# 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
-
-# If configure was run before, rerun it with the old arguments.
-# Otherwise, run configure with argument $PREREQ_OPTIONS.
+# SPKG_COLLECT_FILES contains the files that influence the *runtime* of the
+# portions of the 'configure' script generated by the SAGE_SPKG_COLLECT macro
+SPKG_COLLECT_FILES = build/pkgs/*/package-version.txt build/pkgs/*/dependencies*
+
+# If configure was not run before, complain.
+# If configure is newer than the files it generated (we test build/make/Makefile),
+#    we regenerate config.status by running the "config.status --recheck".
+# Either way we regenerate the generated files by calling "config.status".
 build/make/Makefile: configure $(SPKG_COLLECT_FILES) $(CONFIG_FILES:%=%.in)
-	$(MAKE) reconfigure
+	@if [ -x config.status ]; then				\
+	    case '$?' in					\
+		*configure*|*package-version*|*dependencies*)	\
+		    $(MAKE) reconfigure;;			\
+		*)						\
+		    ./config.status;;				\
+	    esac;						\
+	else							\
+	    $(MAKE) reconfigure;				\
+	fi
 
 reconfigure:
 	rm -f config.log
@@ -324,7 +336,25 @@ ptestoptionallong-nodoc:
 
 ###############################################################################
 
-configure: bootstrap src/doc/bootstrap configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4 build/pkgs/*/type build/pkgs/*/install-requires.txt build/pkgs/*/package-version.txt build/pkgs/*/distros/*.txt
+# The 'configure' script is just one of the files generated by 'bootstrap'.
+# CONFIGURE_DEPENDENCIES is the list of files that influence the generation of 'configure'.
+CONFIGURE_DEPENDENCIES =							\
+	configure.ac src/bin/sage-version.sh m4/*.m4				\
+	build/pkgs/*/spkg-configure.m4						\
+	build/pkgs/*/type build/pkgs/*/SPKG.rst					\
+	build/pkgs/*/checksums.ini build/pkgs/*/requirements.txt		\
+	build/pkgs/*/install-requires.txt build/pkgs/*/package-version.txt	\
+	build/pkgs/*/spkg-install build/pkgs/*/spkg-install.in
+
+# SPKG_INFO_DEPENDENCIES is the list of files that influence the run of 'sage-spkg-info' and hence
+# the generation of the files generated in 'src/doc' by 'src/doc/bootstrap'.
+SPKG_INFO_DEPENDENCIES =							\
+	build/pkgs/*/type build/pkgs/*/SPKG.rst					\
+	build/pkgs/*/requirements.txt						\
+	build/pkgs/*/install-requires.txt build/pkgs/*/package-version.txt	\
+	build/pkgs/*/distros/*.txt
+
+configure: bootstrap src/doc/bootstrap $(CONFIGURE_DEPENDENCIES) $(SPKG_INFO_DEPENDENCIES)
 	./bootstrap -d
 
 install: all