Merge branch 'develop' into precision_in_logexp

Author: xcaruso

.devcontainer/onCreate-conda.sh

@@ -10,5 +10,4 @@ mamba env create -y --file environment-3.11-linux.yml || mamba env update -y --f
 conda init bash
 
 # Build sage
-conda run -n sage-dev ./bootstrap
-conda run -n sage-dev pip install --no-build-isolation -v -v -e ./src
+conda run -n sage-dev pip install --no-build-isolation -v -v -e .

.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
@@ -69,11 +69,23 @@ jobs:
           export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
           export CC="ccache $CC"
           export CXX="ccache $CXX"
-          pip install --no-build-isolation --config-settings=builddir=builddir . -v
+          # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda
+          pip install --no-build-isolation --no-deps --config-settings=builddir=builddir . -v
+
+      - name: Verify dependencies
+        shell: bash -l {0}
+        run: pip check
 
       - name: Test
         shell: bash -l {0}
         run: |
           # We don't install sage_setup, so don't try to test it
           rm -R ./src/sage_setup/
           ./sage -t --all -p4
+
+      - name: Upload log
+        uses: actions/[email protected]
+        if: failure()
+        with:
+          name: ${{ runner.os }}-meson-${{ matrix.python }}-log
+          path: builddir/meson-logs/

.github/workflows/dist.yml

@@ -119,10 +119,38 @@ jobs:
         with:
           name: dist
           path: dist
-      - uses: softprops/action-gh-release@v2
+      - name: Create release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          latest_release_tag=$(curl -s https://api.github.com/repos/${{ github.repository }}/releases \
+          | jq -r 'sort_by(.created_at) | last(.[]).tag_name')
+          release_notes=$(curl -s \
+            -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GITHUB_TOKEN" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/${{ github.repository }}/releases/generate-notes \
+            -d "{
+              \"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" \
+            -H "Authorization: Bearer $GITHUB_TOKEN" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/${{ github.repository }}/releases \
+            -d "{
+              \"tag_name\": \"${{ github.ref_name }}\",
+              \"prerelease\": ${{ contains(github.ref, 'beta') || contains(github.ref, 'rc') }},
+              \"body\": $release_notes
+            }"
+      - name: Create release assets
+        uses: softprops/action-gh-release@v2
         with:
-          generate_release_notes: true
-          prerelease: ${{ contains(github.ref, 'beta') || contains(github.ref, 'rc') }}
           files: |
             dist/*
             upstream/*

.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

@@ -18,7 +18,6 @@
 /config.log
 /config.status
 /configure
-/conftest*
 /confdefs.h
 
 /m4/sage_spkg_configures.m4
@@ -27,13 +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

@@ -18,9 +18,7 @@
     },
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": [
-        "--rootdir=src/sage",
-        "-c=src/tox.ini",
-        "--doctest-modules"
+        "--doctest"
     ],
     "python.testing.unittestEnabled": false,
     "cSpell.words": [
@@ -110,5 +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.beta2
+version: 10.6.beta6
 doi: 10.5281/zenodo.8042260
-date-released: 2024-12-22
+date-released: 2025-02-10
 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
@@ -253,9 +253,19 @@ TEST_TARGET = $@
 
 TEST = ./sage -t --logfile=$(TEST_LOG) $(TEST_FLAGS) --optional=$(TEST_OPTIONAL) $(TEST_FILES)
 
+test-git-no-uncommitted-changes:
+	@UNCOMMITTED=$$(git status --porcelain); \
+	if [ -n "$$UNCOMMITTED" ]; then \
+	    echo "Error: the git repo has uncommitted changes:"; \
+	    echo "$$UNCOMMITTED"; \
+	    echo; \
+	    exit 1; \
+	fi
+
 test: all
 	@echo '### make $(TEST_TARGET): Running $(TEST)' >> $(TEST_LOG)
-	$(TEST)
+	$(TEST); \
+	$(MAKE) test-git-no-uncommitted-changes
 
 check:
 	@$(MAKE) test
@@ -302,7 +312,8 @@ ptestoptionallong:
 test-nodoc: TEST_OPTIONAL := $(TEST_OPTIONAL),!sagemath_doc_html,!sagemath_doc_pdf
 test-nodoc: build
 	@echo '### make $(TEST_TARGET): Running $(TEST)' >> $(TEST_LOG)
-	$(TEST)
+	$(TEST); \
+	$(MAKE) test-git-no-uncommitted-changes
 
 check-nodoc:
 	@$(MAKE) test-nodoc
@@ -387,5 +398,6 @@ list:
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \
+	test-git-no-uncommitted-changes \
 	list \
 	doc-clean clean sagelib-clean build-clean

README.md

@@ -679,7 +679,7 @@ information, patches, and build scripts are in the accompanying
 part of the Sage git repository.
 
 <p align="center">
-   Copyright (C) 2005-2024 The Sage Development Team
+   Copyright (C) 2005-2025 The Sage Development Team
 </p>
 <p align="center">
    https://www.sagemath.org

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.6.beta2, Release Date: 2024-12-22
+SageMath version 10.6.beta6, Release Date: 2025-02-10

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