Merge remote-tracking branch 'origin/develop' into use-pari-zncoppers…

…mith

.github/workflows/build.yml

@@ -29,7 +29,7 @@ concurrency:
 #
 # The three workflows:
 #
-#  - build.yml (with jobs test-new, test-mod, test-long),
+#  - build.yml (with jobs test-new, test-long),
 #  - doc-build.yml,
 #  - doc-build-pdf.yml
 #
@@ -50,7 +50,7 @@ concurrency:
 # This baseline is transparently improved by our use of the GH Actions cache,
 # see https://docs.docker.com/build/ci/github-actions/cache/#cache-backend-api.
 #
-# Jobs test-mod and test-long are only started after test-new completed;
+# Jobs test-long is only started after test-new completed;
 # but the workflows doc-build.yml and doc-build-pdf.yml are started independently.
 #
 #  - When nothing is cached and the 3 workflows are launched in parallel,
@@ -254,104 +254,6 @@ jobs:
           ./sage -t --long --format github -p4 ${{ steps.changed-files.outputs.doctests_all_changed_files }}
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-  test-mod:
-    runs-on: ubuntu-latest
-    needs: [test-new]
-    services:
-      # https://docs.docker.com/build/ci/github-actions/local-registry/
-      registry:
-        image: registry:2
-        ports:
-          - 5000:5000
-    strategy:
-      fail-fast: false
-      matrix:
-        targets:
-          - sagemath_categories-check
-    steps:
-      - name: Maximize build disk space
-        uses: easimon/maximize-build-space@v10
-        with:
-          # need space in /var for Docker images
-          root-reserve-mb:      30000
-          remove-dotnet:        true
-          remove-android:       true
-          remove-haskell:       true
-          remove-codeql:        true
-          remove-docker-images: true
-
-      - name: Checkout
-        id: checkout
-        uses: actions/checkout@v4
-
-      - name: Install test prerequisites
-        # From docker.yml
-        run: |
-          sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
-          sudo apt-get clean
-          df -h
-
-      - name: Merge CI fixes from sagemath/sage
-        # From docker.yml
-        # This step needs to happen after the commit sha is put in DOCKER_TAG
-        # so that multi-stage builds can work correctly.
-        run: |
-          .ci/merge-fixes.sh
-        env:
-          GH_TOKEN: ${{ github.token }}
-
-      # Building
-
-      - name: Generate Dockerfile
-        # From docker.yml
-        run: |
-          tox -e ${{ env.TOX_ENV }}
-          cp .tox/${{ env.TOX_ENV }}/Dockerfile .
-        env:
-          # Only generate the Dockerfile, do not run 'docker build' here
-          DOCKER_TARGETS: ""
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-        with:
-          driver-opts: network=host
-
-      - name: Build Docker image
-        id: image
-        uses: docker/build-push-action@v6
-        with:
-          push:       true
-          load:       false
-          context:    .
-          tags:       ${{ env.BUILD_IMAGE }}
-          target:     with-targets
-          cache-from: type=gha
-          cache-to:   type=gha,mode=max
-          build-args: |
-            NUMPROC=6
-            USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
-            TARGETS_PRE=build/make/Makefile
-            TARGETS=${{ needs.test-new.outputs.build_targets }}
-
-      - name: Start container
-        id: container
-        if: (success() || failure())
-        run: |
-          docker run --name BUILD -dit \
-                     --mount type=bind,src=$(pwd),dst=$(pwd) \
-                     --workdir $(pwd) \
-                     ${{ env.BUILD_IMAGE }} /bin/sh
-
-      # Testing
-
-      - name: Test modularized distributions
-        if: (success() || failure()) && steps.container.outcome == 'success'
-        run: |
-          export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
-          make V=0 tox-ensure && make ${{ matrix.targets }}
-        shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
-
   test-long:
     runs-on: ubuntu-latest
     needs: [test-new]

.github/workflows/ci-conda.yml

@@ -26,23 +26,12 @@ jobs:
         # On pushes to tags or branches, test the whole matrix.
         os: >-
           ${{ github.event_name == 'pull_request'
-                && fromJson('["ubuntu-latest"]')
+                && fromJson('["ubuntu-latest", "macos-latest"]')
                 || fromJson('["ubuntu-latest", "macos-latest", "macos-13"]') }}
-        python: >-
-          ${{ github.event_name == 'pull_request'
-                && fromJson('["3.9"]')
-                || fromJson('["3.9", "3.10", "3.11"]') }}
+        python: ['3.11', '3.12']
         # Optional environment is disabled for now as its not yet working
         # environment: [environment, environment-optional]
         conda-env: [environment]
-        # On pull requests, only test two jobs:
-        # Ubuntu with Python 3.9, macOS (arm64) with Python 3.11.
-        # Build & Test currently uses Python 3.10 (on ubuntu-jammy).
-        # Together, they cover the supported minor Python versions.
-        include: >-
-          ${{ github.event_name == 'pull_request'
-                && fromJson('[{"os": "macos-latest", "python": "3.11", "conda-env": "environment"}]')
-                || fromJson('[]') }}
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/ci-meson.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu]
-        python: ['3.9', '3.10', '3.11']
+        python: ['3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/dist.yml

@@ -135,6 +135,8 @@ jobs:
               \"tag_name\": \"${{ github.ref_name }}\",
               \"previous_tag_name\": \"$latest_release_tag\"
             }" | jq -r '.body')
+          # escape special characters for json
+          release_notes=$(jq -R -s '.' <<< "$release_notes")
           curl -L \
             -X POST \
             -H "Accept: application/vnd.github+json" \
@@ -144,7 +146,7 @@ jobs:
             -d "{
               \"tag_name\": \"${{ github.ref_name }}\",
               \"prerelease\": ${{ contains(github.ref, 'beta') || contains(github.ref, 'rc') }},
-              \"body\": \"$release_notes\"
+              \"body\": $release_notes
             }"
       - name: Create release assets
         uses: softprops/action-gh-release@v2

.github/workflows/pyright.yml

@@ -32,7 +32,7 @@ jobs:
           eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git)
 
       - name: Install GH CLI
-        uses: dev-hanz-ops/[email protected].0
+        uses: dev-hanz-ops/[email protected].1
         with:
           gh-cli-version: 2.32.0
 

.gitignore

@@ -26,13 +26,11 @@
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig
 
-# Conda environment files
-# The files without Python version, with -dev or in src are no longer generated
-# but may still be in users' directories.
+# Conda environment files (auto-generated)
+/environment-3.[0-9].yml
+/environment-3.[0-9][0-9].yml
+# The following files are no longer generated but may still be in users' directories
 /environment.yml
-/environment-3.9.yml
-/environment-3.10.yml
-/environment-3.11.yml
 /environment-dev-3.9.yml
 /environment-dev-3.10.yml
 /environment-dev-3.11.yml

.vscode/settings.json

@@ -108,5 +108,11 @@
         "zmin"
     ],
     "editor.formatOnType": true,
-    "esbonio.sphinx.confDir": ""
+    "esbonio.sphinx.confDir": "",
+    // Don't update the settings.json file with values inferred from Meson (we provide them manually)
+    "mesonbuild.modifySettings": false,
+    // Use the Meson build system for C/C++ files
+    "C_Cpp.default.configurationProvider": "mesonbuild.mesonbuild",
+    // Use the compile_commands.json file generated by Meson for IntelliSense
+    "C_Cpp.default.compileCommands": "${workspaceFolder}/builddir/compile_commands.json"
 }

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.6.beta3
+version: 10.6.beta5
 doi: 10.5281/zenodo.8042260
-date-released: 2025-01-04
+date-released: 2025-01-26
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

Makefile

@@ -173,7 +173,7 @@ distclean: build-clean
 bootstrap-clean:
 	rm -rf config/install-sh config/compile config/config.guess config/config.sub config/missing configure build/make/Makefile-auto.in
 	rm -f src/doc/en/installation/*.txt
-	find src/doc/en/reference/spkg -name index.rst -prune -o -maxdepth 1 -name "*.rst" -exec rm -f {} \+
+	find src/doc/en/reference/spkg -maxdepth 1 -name index.rst -prune -o -name "*.rst" -exec rm -f {} \+
 	for a in environment environment-optional src/environment src/environment-optional; do rm -f $$a.yml $$a-3.[89].yml $$a-3.1[0-9].yml; done
 	rm -f src/requirements.txt
 	rm -f src/setup.cfg

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.6.beta3, Release Date: 2025-01-04
+SageMath version 10.6.beta5, Release Date: 2025-01-26

bootstrap

@@ -224,8 +224,8 @@ save () {
 	config/install-sh config/compile config/config.guess config/config.sub config/missing \
 	build/make/Makefile-auto.in \
 	src/doc/en/installation/*.txt \
-	$(find src/doc/en/reference/spkg -name index.rst -prune -o -maxdepth 1 -name "*.rst" -print) \
-	environment-3.[89]-*.yml environment-3.1[0-9]-*.yml \
+	$(find src/doc/en/reference/spkg -maxdepth 1 -name index.rst -prune -o -name "*.rst" -print) \
+	environment-3.1[0-9]-*.yml \
 	src/pyproject.toml \
 	src/requirements.txt \
 	src/setup.cfg \

build/bin/sage-spkg

@@ -603,14 +603,14 @@ case "$PKG_SRC" in
 esac
 
 # Poison the proxy variable to forbid downloads in spkg-install
-# for normal packages
-case $PKG_SRC_TYPE in
-  normal|wheel)
-    export http_proxy=http://192.0.2.0:5187/
-    export https_proxy=$http_proxy
-    export ftp_proxy=$http_proxy
-    export rsync_proxy=$http_proxy
-    ;;
+# for normal/wheel standard packages
+case "$PKG_TYPE:$PKG_SRC_TYPE" in
+    standard:normal|standard:wheel)
+        export http_proxy=http://192.0.2.0:5187/
+        export https_proxy=$http_proxy
+        export ftp_proxy=$http_proxy
+        export rsync_proxy=$http_proxy
+        ;;
 esac
 
 # Make sage-logger show the full logs

build/pkgs/ccache/spkg-install.in

@@ -4,7 +4,6 @@ mkdir build
 cd build
 sdh_cmake -DCMAKE_BUILD_TYPE=Release \
           -DENABLE_TESTING=OFF \
-		  -DREDIS_STORAGE_BACKEND=OFF \
 		  ..
 sdh_make
 sdh_make_install

build/pkgs/configure/checksums.ini

@@ -1,3 +1,3 @@
 tarball=configure-VERSION.tar.gz
-sha1=852d0d200a6a73aa5ddb9e00874cbe4a61c211e9
-sha256=c4b089d90850dfdf15b905f66e4f6a0d961b96eb0663d8603beaff1a9efb2cbe
+sha1=86711d4cbef2cd4e7bb4afcde36965e5dea908e0
+sha256=9793cf92ebdceb09050a585294de93c242c033745a0012cae1bd301d307a45df

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-a2ba1f943f88775218c385efe55509c4548d1b44
+efc0914cd8d72a9bdfdcca4511b55e290b9b6674

build/pkgs/igraph/checksums.ini

@@ -1,4 +1,4 @@
 tarball=igraph-VERSION.tar.gz
-sha1=3789f61beac1f1231f8c3832102dcb2720f2a0c9
-sha256=b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625
+sha1=af74e361167bd790ed2fcc248acd21ec946ddb2a
+sha256=03ba01db0544c4e32e51ab66f2356a034394533f61b4e14d769b9bbf5ad5e52c
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz

build/pkgs/igraph/package-version.txt

@@ -1 +1 @@
-0.10.12
+0.10.15

build/pkgs/igraph/spkg-configure.m4

@@ -3,7 +3,7 @@ SAGE_SPKG_CONFIGURE([igraph], [
     dnl check for igraph with pkg-config
     dnl Per upstream in https://github.com/sagemath/sage/pull/36750#issuecomment-1826998762:
     dnl each python-igraph release is only guaranteed to be compatible with the same C/igraph that it bundles
-    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.12 igraph < 0.10.13], [], [
+    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.14 igraph < 0.10.16], [], [
         sage_spkg_install_igraph=yes])
   ])
 ])

build/pkgs/ore_algebra/requirements.txt

@@ -1 +1 @@
-git+https://github.com/mkauers/ore_algebra@01c357f590685ff362c008229681ee08269457da#egg=ore_algebra
+ore_algebra @ git+https://github.com/mkauers/ore_algebra

build/pkgs/python_igraph/checksums.ini

@@ -1,4 +1,4 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=da963213ab22c60938d4e77ffab811875ee43a8a
-sha256=2d71d645a4c3344c5910543fabbae10d3163f46a3e824ba7753c14b9036b8233
+sha1=19b52531169f200ff60f2cb8245eaa9e277c6c13
+sha256=d7dc1404567ba3b0ea1bf8b5fa6e101617915c8ad11ea5a9f925a40bf4adad7d
 upstream_url=https://files.pythonhosted.org/packages/source/i/igraph/igraph-VERSION.tar.gz

build/pkgs/python_igraph/package-version.txt

@@ -1 +1 @@
-0.11.5
+0.11.8

build/pkgs/sage_conf/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-conf ~= 10.6b3
+sage-conf ~= 10.6b5

build/pkgs/sage_docbuild/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-docbuild ~= 10.6b3
+sage-docbuild ~= 10.6b5

build/pkgs/sage_setup/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-setup ~= 10.6b3
+sage-setup ~= 10.6b5

build/pkgs/sage_sws2rst/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-sws2rst ~= 10.6b3
+sage-sws2rst ~= 10.6b5

build/pkgs/sagelib/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-standard ~= 10.6b3
+sagemath-standard ~= 10.6b5

build/pkgs/sagemath_bliss/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-bliss ~= 10.6b3
+sagemath-bliss ~= 10.6b5

build/pkgs/sagemath_categories/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-categories ~= 10.6b3
+sagemath-categories ~= 10.6b5

build/pkgs/sagemath_coxeter3/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-coxeter3 ~= 10.6b3
+sagemath-coxeter3 ~= 10.6b5

build/pkgs/sagemath_environment/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-environment ~= 10.6b3
+sagemath-environment ~= 10.6b5

build/pkgs/sagemath_mcqd/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-mcqd ~= 10.6b3
+sagemath-mcqd ~= 10.6b5

build/pkgs/sagemath_meataxe/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-meataxe ~= 10.6b3
+sagemath-meataxe ~= 10.6b5

build/pkgs/sagemath_objects/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-objects ~= 10.6b3
+sagemath-objects ~= 10.6b5

build/pkgs/sagemath_repl/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-repl ~= 10.6b3
+sagemath-repl ~= 10.6b5

build/pkgs/sagemath_sirocco/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-sirocco ~= 10.6b3
+sagemath-sirocco ~= 10.6b5

build/pkgs/sagemath_tdlib/version_requirements.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-tdlib ~= 10.6b3
+sagemath-tdlib ~= 10.6b5

build/sage_bootstrap/download/mirror_list.py

@@ -170,7 +170,8 @@ def _rank_mirrors(self):
         This method is used by the YUM fastestmirror plugin
         """
         timed_mirrors = []
-        import time, socket
+        import time
+        import socket
         log.info('Searching fastest mirror')
         timeout = 1
         for mirror in self.mirrors: