Merge branch 'develop' into quatalg_from_ramification

.ci/create-changes-html.sh

@@ -16,6 +16,12 @@ echo '<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highli
 echo '<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/highlight.min.js"></script>' >> CHANGES.html
 echo '<script>hljs.highlightAll();</script>' >> CHANGES.html
 cat >> CHANGES.html << EOF
+<style>
+  p.diff a:first-child {
+    font-weight: bold;
+    font-size: x-large;
+  }
+</style>
 <script>
 document.addEventListener('DOMContentLoaded', () => {
 // This URL is hardcoded in the file .github/workflows/doc-publish.yml.

.ci/write-dockerfile.sh

@@ -275,11 +275,11 @@ cat <<EOF
 FROM with-system-packages AS bootstrapped
 #:bootstrapping:
 RUN rm -rf /new /sage/.git
-$ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-conda configure.ac sage .homebrew-build-env tox.ini Pipfile.m4 .gitignore /new/
+$ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap configure.ac sage .homebrew-build-env tox.ini .gitignore /new/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
 $ADD src/bin /new/src/bin
-$ADD src/Pipfile.m4 src/pyproject.toml src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt /new/src/
+$ADD src/pyproject.toml src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt /new/src/
 $ADD m4 /new/m4
 $ADD pkgs /new/pkgs
 $ADD build /new/build
@@ -326,7 +326,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:toolchain:
 $RUN$CHECK_STATUS_THEN make \${USE_MAKEFLAGS} base-toolchain$ENDRUN$THEN_SAVE_STATUS
 
@@ -335,7 +335,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:make:
 ARG TARGETS_PRE="all-sage-local"
 $RUN$CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_PRE}$ENDRUN$THEN_SAVE_STATUS
@@ -345,7 +345,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 $ADD .gitignore /new/.gitignore
 $ADD src /new/src
 RUN cd /new && rm -rf .git && \\
@@ -366,7 +366,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 ARG TARGETS_OPTIONAL="ptest"
 $RUN$CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_OPTIONAL} || echo "(error ignored)"$ENDRUN$THEN_SAVE_STATUS
 

.codecov.yml

@@ -17,3 +17,4 @@ coverage:
         target: auto
         threshold: 0%
         base: auto
+        informational: true

.devcontainer/onCreate-conda.sh

@@ -2,10 +2,12 @@
 set -e
 
 # Create conda environment
-conda install mamba -n base -c conda-forge -y
-mamba env create --file src/environment-dev-3.11-linux.yml || mamba env update --file src/environment-dev-3.11-linux.yml
+conda config --env --add channels conda-forge
+conda config --env --set channel_priority strict
+conda update -y --all --override-channels -c conda-forge
+conda install mamba=1 -n base -y
+mamba env create -y --file environment-3.11-linux.yml || mamba env update -y --file environment-3.11-linux.yml
 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]
@@ -589,6 +491,6 @@ jobs:
 
       - name: Upload coverage to codecov
         if: (success() || failure()) && steps.container.outcome == 'success'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           directory: .coverage/coverage-report

.github/workflows/changelog_trigger.yml

@@ -0,0 +1,23 @@
+name: Trigger Changelog Generation
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  trigger-website-repo-workflow:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger Generate Changelog Workflow in website repo
+        if: "!github.event.release.prerelease"
+        env:
+          GITHUB_PAT: ${{ secrets.WEBSITE_ACCESS_TOKEN }}
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+        run: |
+          curl -L \
+            -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GITHUB_PAT" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/sagemath/website/actions/workflows/generate_changelog.yml/dispatches \
+            -d '{"ref":"master","inputs":{"release_tag":"'"$RELEASE_TAG"'"}}'

.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
@@ -59,7 +48,7 @@ jobs:
         with:
           path: ~/conda_pkgs_dir
           key:
-            ${{ runner.os }}-conda-${{ hashFiles('src/environment-3.11.yml') }}
+            ${{ runner.os }}-conda-${{ hashFiles('environment-3.11.yml') }}
 
       - name: Setup Conda environment
         uses: conda-incubator/setup-miniconda@v3
@@ -69,8 +58,8 @@ jobs:
           use-mamba: true
           channels: conda-forge
           channel-priority: true
-          activate-environment: sage
-          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && (startsWith(runner.arch, 'ARM') && 'macos' || 'macos-x86_64') || 'linux' }}.yml
+          activate-environment: sage-dev
+          environment-file: ${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && (startsWith(runner.arch, 'ARM') && 'macos' || 'macos-x86_64') || 'linux' }}.yml
 
       - name: Print Conda environment
         shell: bash -l {0}

.github/workflows/ci-linux.yml

@@ -50,6 +50,7 @@ jobs:
       tox_packages_factors: >-
         ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
+      logs_artifact: false
 
   # All platforms. This duplicates the default platform, but why not,
   # it makes it more robust regarding random timeouts.

.github/workflows/ci-macos.yml

@@ -95,7 +95,7 @@ jobs:
       - name: make dist
         run: |
           ./configure --enable-download-from-upstream-url && make dist
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: "dist/*.tar.gz"
           name: dist
@@ -119,7 +119,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         if: "!contains(matrix.tox_system_factor, 'nobootstrap')"
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           path: .
           name: dist
@@ -147,7 +147,7 @@ jobs:
         run: |
           mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"
         if: always()
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: artifacts
           name: ${{ env.LOGS_ARTIFACT_NAME }}