Merge branch 'develop' into macaulay

Author: xcaruso

.github/workflows/build.yml

@@ -107,6 +107,8 @@ jobs:
         uses: tj-actions/changed-files@v45
         with:
           # File extensions for doctests per sage.doctest.control.skipfile
+          # Also src/sage/doctests/tests/ are excluded because of nodoctest file
+          # which would make sage.doctest.control.skipdir return True
           files_yaml: |
             configures:
               - 'build/pkgs/*/spkg-configure.m4'
@@ -118,6 +120,7 @@ jobs:
             doctests:
               - 'src/**/*.{py,pyx,pxd,pxi,sage,spyx,rst,tex}'
               - '!src/{setup,conftest*}.py'
+              - '!src/sage/doctest/tests/*'
 
       - name: Determine targets to build
         id: build-targets
@@ -246,7 +249,7 @@ jobs:
           ./sage -python -m pytest -c tox.ini -qq --doctest --collect-only || true
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Test changed files (sage -t --new)
+      - name: Test changed files
         if: (success() || failure()) && steps.container.outcome == 'success' && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4

.github/workflows/ci-linux-incremental.yml

@@ -1,6 +1,6 @@
 name: CI Linux incremental
 
-## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with select environments,
+## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with selected environments,
 ## whenever a GitHub pull request is opened or synchronized in a repository
 ## where GitHub Actions are enabled.
 ##
@@ -99,56 +99,9 @@ jobs:
          "debian-bullseye",
          "debian-bookworm",
          "fedora-30",
-         "fedora-40",
-         "gentoo-python3.11",
-         "debian-bullseye-i386"]
+         "fedora-40",]
       tox_packages_factors: >-
           ["standard",
            "minimal"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
       max_parallel: 8
-
-  constraints_pkgs-norequirements:
-    needs: [changed_files]
-    uses: ./.github/workflows/docker.yml
-    with:
-      # Build incrementally from published Docker image
-      incremental: true
-      free_disk_space: true
-      from_docker_repository: ghcr.io/sagemath/sage/
-      from_docker_target: "with-targets-pre"
-      from_docker_tag: "dev"
-      docker_targets: "with-targets-pre"
-      targets_pre: "${{needs.changed_files.outputs.build_targets}} all-sage-local python3-ensure tox-ensure sagelib-tox-sagepython-constraints_pkgs-norequirements"
-      tox_system_factors: >-
-        ["ubuntu-focal",
-         "ubuntu-noble",
-         "debian-bookworm",
-         "fedora-40",
-         "debian-bullseye-i386"]
-      tox_packages_factors: >-
-          ["standard"]
-      docker_push_repository: ghcr.io/${{ github.repository }}/
-      max_parallel: 16
-
-  site:
-    needs: [changed_files]
-    uses: ./.github/workflows/docker.yml
-    with:
-      # Build incrementally from published Docker image
-      incremental: true
-      free_disk_space: true
-      from_docker_repository: ghcr.io/sagemath/sage/
-      from_docker_target: "with-targets"
-      from_docker_tag: "dev"
-      docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
-      # Only test systems with a usable system python (>= 3.9)
-      # with only a small number of test failures as of 10.2.rc0
-      tox_system_factors: >-
-        ["gentoo-python3.11",
-         "archlinux-latest",
-         "fedora-40"]
-      tox_packages_factors: >-
-          ["standard-sitepackages"]
-      docker_push_repository: ghcr.io/${{ github.repository }}/

.github/workflows/ci-linux.yml

@@ -1,8 +1,7 @@
 name: CI Linux
 
-## 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.
+## This GitHub Actions workflow runs SAGE_ROOT/tox.ini with selected environments,
+## whenever a tag is pushed.
 ##
 ## It builds and checks some sage spkgs as defined in TARGETS.
 ##
@@ -33,29 +32,7 @@ permissions:
   packages: write
 
 jobs:
-
-  # standard (without ptest) for the default platform (used by build.yml etc.)
-  default:
-    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
-      targets: build doc-html
-      targets_optional: ptest
-      tox_system_factors: >-
-        ["ubuntu-jammy"]
-      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.
-
-  standard:
+  minimal:
     if: ${{ success() || failure() }}
     uses: ./.github/workflows/docker.yml
     with:
@@ -66,124 +43,21 @@ jobs:
       targets_pre: all-sage-local
       targets: build doc-html
       targets_optional: ptest
+      tox_system_factors: >-
+          ["ubuntu-jammy"]
       tox_packages_factors: >-
-          ["standard"]
+          ["minimal"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
-      # Make sure that all "standard" jobs can start simultaneously,
-      # so that runners are available by the time that "default" starts.
-      max_parallel: 50
-
-  standard-constraints_pkgs-norequirements:
-    if: ${{ success() || failure() }}
-    needs: [standard]
-    uses: ./.github/workflows/docker.yml
-    with:
-      # Build incrementally from previous stage (pre)
-      incremental: true
-      free_disk_space: true
-      from_docker_repository: ghcr.io/${{ github.repository }}/
-      from_docker_target: "with-targets-pre"
-      docker_targets: "with-targets-pre"
-      targets_pre: all-sage-local python3-ensure tox-ensure sagelib-tox-sagepython-constraints_pkgs-norequirements
-      tox_packages_factors: >-
-          ["standard"]
-      max_parallel: 15
 
-  standard-sitepackages:
-    if: ${{ success() || failure() }}
-    needs: [standard]
+  standard:
     uses: ./.github/workflows/docker.yml
     with:
-      # Build incrementally from previous stage (pre)
-      incremental: true
       free_disk_space: true
-      from_docker_repository: ghcr.io/${{ github.repository }}/
-      from_docker_target: "with-targets-pre"
-      docker_targets: "with-targets with-targets-optional"
-      # FIXME: duplicated from env.TARGETS
-      targets: build doc-html
-      targets_optional: ptest
-      tox_packages_factors: >-
-        ["standard-sitepackages"]
-      # Only test systems with a usable system python (>= 3.9)
-      tox_system_factors: >-
-        ["ubuntu-jammy",
-         "ubuntu-lunar",
-         "ubuntu-mantic",
-         "debian-bookworm",
-         "debian-trixie",
-         "debian-sid",
-         "linuxmint-21.1",
-         "linuxmint-21.2",
-         "fedora-40",
-         "centos-stream-9-python3.9",
-         "almalinux-8-python3.9",
-         "gentoo-python3.10",
-         "gentoo-python3.11",
-         "archlinux-latest",
-         "opensuse-15.5-gcc_11-python3.11",
-         "opensuse-tumbleweed-python3.10",
-         "opensuse-tumbleweed"]
-      docker_push_repository: ghcr.io/${{ github.repository }}/
-      max_parallel: 8
-
-  minimal:
-    if: ${{ success() || failure() }}
-    uses: ./.github/workflows/docker.yml
-    with:
       # Build from scratch
-      free_disk_space: true
       docker_targets: "with-system-packages configured with-targets-pre with-targets with-targets-optional"
-      # FIXME: duplicated from env.TARGETS
       targets_pre: all-sage-local
       targets: build doc-html
       targets_optional: ptest
       tox_packages_factors: >-
-          ["minimal"]
-      docker_push_repository: ghcr.io/${{ github.repository }}/
-      # Reduced from 30 because it may run in parallel with 'standard' and 'standard-sitepackages' above.
-      # Calibrated for clogging the job pipeline until the "default" job has finished.
-      max_parallel: 24
-
-  maximal-pre:
-    if: ${{ success() || failure() }}
-    needs: [minimal]
-    uses: ./.github/workflows/docker.yml
-    with:
-      free_disk_space: true
-      # Build from scratch
-      docker_targets: "with-system-packages configured with-targets-pre"
-      # FIXME: duplicated from env.TARGETS
-      targets_pre: all-sage-local
-      tox_packages_factors: >-
-          ["maximal"]
+          ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
-
-  optional:
-    if: ${{ success() || failure() }}
-    needs: [maximal-pre]
-    uses: ./.github/workflows/docker.yml
-    with:
-      incremental: true
-      free_disk_space: true
-      from_docker_repository: ghcr.io/${{ github.repository }}/
-      from_docker_target: "with-targets-pre"
-      tox_packages_factors: >-
-          ["maximal"]
-      docker_targets: "with-targets-optional"
-      # We remove packages starting with _, in particular package _develop
-      targets_optional: '$(echo $(export PATH=build/bin:$PATH && sage-package list :optional: --has-file "spkg-install.in|spkg-install|requirements.txt" --no-file "huge|has_nonfree_dependencies" | grep -v sagemath_doc | grep -v ^_))'
-
-  experimental:
-    if: ${{ success() || failure() }}
-    needs: [optional]
-    uses: ./.github/workflows/docker.yml
-    with:
-      incremental: true
-      free_disk_space: true
-      from_docker_repository: ghcr.io/${{ github.repository }}/
-      from_docker_target: "with-targets-pre"
-      tox_packages_factors: >-
-          ["maximal"]
-      docker_targets: "with-targets-optional"
-      targets_optional: '$(echo $(export PATH=build/bin:$PATH && sage-package list :experimental: --has-file "spkg-install.in|spkg-install|requirements.txt" --no-file "huge|has_nonfree_dependencies" | grep -v sagemath_doc))'

.github/workflows/ci-macos.yml

@@ -99,61 +99,3 @@ jobs:
         with:
           path: "dist/*.tar.gz"
           name: dist
-
-  local-macos-nohomebrew:
-
-    needs: [dist]
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      max-parallel: 4
-      matrix:
-        os: [ macos-12, macos-13, macos-14 ]
-        tox_system_factor: [macos-nobootstrap]
-        tox_packages_factor: [minimal]
-        xcode_version_factor: [default]
-    env:
-      TOX_ENV: local-${{ 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 }}-xcode_${{ matrix.xcode_version_factor }}
-    steps:
-      - uses: actions/checkout@v4
-        if: "!contains(matrix.tox_system_factor, 'nobootstrap')"
-      - uses: actions/download-artifact@v4
-        with:
-          path: .
-          name: dist
-        if: contains(matrix.tox_system_factor, 'nobootstrap')
-      - name: Unpack sage dist
-        run: |
-          tar xf sage*.tar.gz --strip-components=1
-        if: contains(matrix.tox_system_factor, 'nobootstrap')
-      - name: Move homebrew away
-        run: |
-          (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
-      - name: Install test prerequisites
-        run: |
-          sudo /usr/bin/python3 -m pip install tox
-      - 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: |
-          (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"
-        if: always()
-      - uses: actions/upload-artifact@v4
-        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()

.github/workflows/ci-meson.yml

@@ -16,14 +16,21 @@ concurrency:
 
 jobs:
   test:
-    name: Conda (${{ matrix.os }}, Python ${{ matrix.python }})
+    name: Conda (${{ matrix.os }}, Python ${{ matrix.python }}${{ matrix.editable && ', editable' || '' }})
     runs-on: ${{ matrix.os }}-latest
 
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu]
         python: ['3.11', '3.12']
+        editable:
+          ${{ fromJson(github.event_name == 'pull_request' && '[false]' || '[false, true]') }}
+        include:
+          # one additional editable run in pull_request, this has no effect if not pull_request
+          - os: ubuntu
+            python: 3.12
+            editable: true
 
     steps:
       - uses: actions/checkout@v4
@@ -70,7 +77,7 @@ jobs:
           export CC="ccache $CC"
           export CXX="ccache $CXX"
           # 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
+          pip install --no-build-isolation --no-deps --config-settings=builddir=builddir ${{ matrix.editable && '--editable' || '' }} . -v
 
       - name: Check update-meson
         # this step must be after build, because meson.build creates a number of __init__.py files
@@ -93,12 +100,14 @@ jobs:
         shell: bash -l {0}
         run: |
           # We don't install sage_setup, so don't try to test it
-          rm -R ./src/sage_setup/
+          # If editable then deleting the directory will cause sage to detect rebuild, which will cause ninja to fail
+          # so we don't delete the directory in this case
+          ${{ matrix.editable && 'true' || 'rm -R ./src/sage_setup/' }}
           ./sage -t --all -p4 --format github
 
       - name: Upload log
         uses: actions/[email protected]
         if: failure()
         with:
-          name: ${{ runner.os }}-meson-${{ matrix.python }}-log
+          name: ${{ runner.os }}-meson-${{ matrix.python }}${{ matrix.editable && '-editable' || '' }}-log
           path: builddir/meson-logs/

.github/workflows/doc-build.yml

@@ -230,6 +230,7 @@ jobs:
                                                   -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d' \
                                                   -e 's;#L[0-9]*";";' \
                                                   -e 's;tab-set--[0-9]*-;tab-set-;' \
+                                                  -e 's;"tab-set--[0-9]*";"tab-set";' \
              && git commit -a -m 'wipe-out')
             # Since HEAD is at commit 'wipe-out', HEAD~1 is commit 'new' (new doc), HEAD~2 is commit 'old' (old doc)
             (cd doc && git diff $(git rev-parse HEAD~2) -- "*.html") > diff.txt