Merge branch 'develop' into pyproject-sagelib

sagemath · Apr 28, 2024 · e8a5733 · e8a5733
2 parents 744da89 + c4363fc
commit e8a5733
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diff --git a/.devcontainer/onCreate-conda.sh b/.devcontainer/onCreate-conda.sh
@@ -8,6 +8,4 @@ conda init bash
 
 # Build sage
 conda run -n sage-dev ./bootstrap
-conda run -n sage-dev ./configure --with-python=/opt/conda/envs/sage-dev/bin/python --prefix=/opt/conda/envs/sage-dev
-conda run -n sage-dev pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup 
 conda run -n sage-dev pip install --no-build-isolation -v -v -e ./src
diff --git a/...toolchain-gcc_9-minimal/devcontainer.json → ...ility-fedora-40-minimal/devcontainer.json b/...toolchain-gcc_9-minimal/devcontainer.json → ...ility-fedora-40-minimal/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "ubuntu-trusty-toolchain-gcc_9-minimal (≥ 8-core)",
+    "name": "fedora-40-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "ubuntu-trusty-toolchain-gcc_9",
+            "SYSTEM_FACTOR": "fedora-40",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...-python3.9-minimal/portability-Dockerfile → ...-fedora-40-minimal/portability-Dockerfile b/...-python3.9-minimal/portability-Dockerfile → ...-fedora-40-minimal/portability-Dockerfile
diff --git a/...oolchain-gcc_9-standard/devcontainer.json → ...lity-fedora-40-standard/devcontainer.json b/...oolchain-gcc_9-standard/devcontainer.json → ...lity-fedora-40-standard/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "ubuntu-trusty-toolchain-gcc_9-standard (≥ 8-core)",
+    "name": "fedora-40-standard (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "ubuntu-trusty-toolchain-gcc_9",
+            "SYSTEM_FACTOR": "fedora-40",
             "PACKAGE_FACTOR": "standard",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...python3.9-standard/portability-Dockerfile → ...fedora-40-standard/portability-Dockerfile b/...python3.9-standard/portability-Dockerfile → ...fedora-40-standard/portability-Dockerfile
diff --git a/...cc_11-python3.9-minimal/devcontainer.json → ...ntoo-python3.12-minimal/devcontainer.json b/...cc_11-python3.9-minimal/devcontainer.json → ...ntoo-python3.12-minimal/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "opensuse-15.3-gcc_11-python3.9-minimal (≥ 8-core)",
+    "name": "gentoo-python3.12-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "opensuse-15.3-gcc_11-python3.9",
+            "SYSTEM_FACTOR": "gentoo-python3.12",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...python3.10-minimal/portability-Dockerfile → ...python3.12-minimal/portability-Dockerfile b/...python3.10-minimal/portability-Dockerfile → ...python3.12-minimal/portability-Dockerfile
diff --git a/...c_11-python3.9-standard/devcontainer.json → ...too-python3.12-standard/devcontainer.json b/...c_11-python3.9-standard/devcontainer.json → ...too-python3.12-standard/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "opensuse-15.3-gcc_11-python3.9-standard (≥ 8-core)",
+    "name": "gentoo-python3.12-standard (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "opensuse-15.3-gcc_11-python3.9",
+            "SYSTEM_FACTOR": "gentoo-python3.12",
             "PACKAGE_FACTOR": "standard",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...ython3.10-standard/portability-Dockerfile → ...ython3.12-standard/portability-Dockerfile b/...ython3.10-standard/portability-Dockerfile → ...ython3.12-standard/portability-Dockerfile
diff --git a/...c_11-python3.10-minimal/devcontainer.json → ...-linuxmint-21.3-minimal/devcontainer.json b/...c_11-python3.10-minimal/devcontainer.json → ...-linuxmint-21.3-minimal/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "opensuse-15.4-gcc_11-python3.10-minimal (≥ 8-core)",
+    "name": "linuxmint-21.3-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "opensuse-15.4-gcc_11-python3.10",
+            "SYSTEM_FACTOR": "linuxmint-21.3",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...hain-gcc_9-minimal/portability-Dockerfile → ...xmint-21.3-minimal/portability-Dockerfile b/...hain-gcc_9-minimal/portability-Dockerfile → ...xmint-21.3-minimal/portability-Dockerfile
diff --git a/..._11-python3.10-standard/devcontainer.json → ...linuxmint-21.3-standard/devcontainer.json b/..._11-python3.10-standard/devcontainer.json → ...linuxmint-21.3-standard/devcontainer.json
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "opensuse-15.4-gcc_11-python3.10-standard (≥ 8-core)",
+    "name": "linuxmint-21.3-standard (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "opensuse-15.4-gcc_11-python3.10",
+            "SYSTEM_FACTOR": "linuxmint-21.3",
             "PACKAGE_FACTOR": "standard",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"

diff --git a/...ain-gcc_9-standard/portability-Dockerfile → ...mint-21.3-standard/portability-Dockerfile b/...ain-gcc_9-standard/portability-Dockerfile → ...mint-21.3-standard/portability-Dockerfile
diff --git a/.devcontainer/portability-ubuntu-noble-minimal/devcontainer.json b/.devcontainer/portability-ubuntu-noble-minimal/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "ubuntu-noble-minimal (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "ubuntu-noble",
+            "PACKAGE_FACTOR": "minimal",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/.devcontainer/portability-ubuntu-noble-minimal/portability-Dockerfile b/.devcontainer/portability-ubuntu-noble-minimal/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/.devcontainer/portability-ubuntu-noble-standard/devcontainer.json b/.devcontainer/portability-ubuntu-noble-standard/devcontainer.json
@@ -0,0 +1,25 @@
+// The command "tox -e update_docker_platforms"
+//   creates .devcontainer/portability-*-*/devcontainer.json
+//      from .devcontainer/portability-devcontainer.json.in
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "ubuntu-noble-standard (≥ 8-core)",
+    "build": {
+        "dockerfile": "portability-Dockerfile",
+        // See tox.ini for definitions
+        "args": {
+            "SYSTEM_FACTOR": "ubuntu-noble",
+            "PACKAGE_FACTOR": "standard",
+            "DOCKER_TARGET": "with-targets",
+            "DOCKER_TAG": "dev"
+        }
+    },
+    "containerEnv": {
+        "MAKE": "make -j4"
+    },
+    "onCreateCommand": ".devcontainer/onCreate.sh",
+    "updateContentCommand": ".devcontainer/portability-updateContent.sh",
+    "extensions": [
+        "ms-python.python"
+    ]
+}
diff --git a/.devcontainer/portability-ubuntu-noble-standard/portability-Dockerfile b/.devcontainer/portability-ubuntu-noble-standard/portability-Dockerfile
@@ -0,0 +1 @@
+../portability-Dockerfile
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,7 +15,7 @@
 - [ ] The description explains in detail what this PR is about.
 - [ ] I have linked a relevant issue or discussion.
 - [ ] I have created tests covering the changes.
-- [ ] I have updated the documentation accordingly.
+- [ ] I have updated the documentation and checked the documentation preview.
 
 ### :hourglass: Dependencies
 

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -15,7 +15,7 @@ on:
       platform:
         description: 'Platform'
         required: true
-        default: 'ubuntu-focal-standard'
+        default: 'ubuntu-jammy-standard'
       docker_tag:
         description: 'Docker tag'
         required: true
@@ -52,7 +52,7 @@ jobs:
 
   build:
     runs-on: ubuntu-latest
-    container: ghcr.io/sagemath/sage/sage-${{ github.event.inputs.platform || 'ubuntu-focal-standard' }}-with-targets:${{ github.event.inputs.docker_tag || 'dev'}}
+    container: ghcr.io/sagemath/sage/sage-${{ github.event.inputs.platform || 'ubuntu-jammy-standard' }}-with-targets:${{ github.event.inputs.docker_tag || 'dev'}}
     needs: [get_ci_fixes]
     steps:
       - name: Checkout
@@ -93,16 +93,16 @@ jobs:
           ./bootstrap && make build
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2 --output-sync=recurse
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4 --output-sync=recurse
+          SAGE_NUM_THREADS: 4
 
       - name: Build modularized distributions
         if: (success() || failure()) && steps.worktree.outcome == 'success'
         run: make V=0 tox && make SAGE_CHECK=no pypi-wheels
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2 --output-sync=recurse
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4 --output-sync=recurse
+          SAGE_NUM_THREADS: 4
 
       - name: Static code check with pyright
         if: (success() || failure()) && steps.worktree.outcome == 'success'
@@ -137,8 +137,8 @@ jobs:
           ./bootstrap && make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage && ./config.status
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4
+          SAGE_NUM_THREADS: 4
 
       - name: Build
         # This step is needed because building the modularized distributions installs some optional packages,
@@ -149,8 +149,8 @@ jobs:
           make build
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2 --output-sync=recurse
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4 --output-sync=recurse
+          SAGE_NUM_THREADS: 4
 
       # Testing
 
@@ -161,16 +161,16 @@ jobs:
           ./sage -t --new -p2
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2 --output-sync=recurse
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4 --output-sync=recurse
+          SAGE_NUM_THREADS: 4
 
       - name: Test modularized distributions
         if: (success() || failure()) && steps.build.outcome == 'success'
         run: make V=0 tox && make pypi-wheels-check
         working-directory: ./worktree-image
         env:
-          MAKE: make -j2 --output-sync=recurse
-          SAGE_NUM_THREADS: 2
+          MAKE: make -j4 --output-sync=recurse
+          SAGE_NUM_THREADS: 4
 
       - name: Check that all modules can be imported
         run: |

diff --git a/.github/workflows/ci-conda.yml b/.github/workflows/ci-conda.yml
@@ -35,12 +35,12 @@ jobs:
         # environment: [environment, environment-optional]
         conda-env: [environment]
         # On pull requests, only test two jobs:
-        # Ubuntu with Python 3.9, macOS with Python 3.10.
-        # Build & Test currently uses Python 3.11 (on ubuntu-focal).
+        # Ubuntu with Python 3.9, macOS 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", "python": "3.10", "conda-env": "environment"}]')
+                && fromJson('[{"os": "macos", "python": "3.11", "conda-env": "environment"}]')
                 || fromJson('[]') }}
 
     steps:
@@ -54,7 +54,7 @@ jobs:
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
 
       - name: Cache conda packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/conda_pkgs_dir
           key:
@@ -77,21 +77,16 @@ jobs:
           conda info
           conda list
 
-      - name: Configure
+      - name: Bootstrap
         shell: bash -l {0}
         continue-on-error: true
         run: |
           ./bootstrap
-          echo "::add-matcher::.github/workflows/configure-systempackage-problem-matcher.json"
-          ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX --enable-system-site-packages $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt --exclude rpy2); do echo --with-system-$pkg=force; done)
-          echo "::remove-matcher owner=configure-system-package-warning::"
-          echo "::remove-matcher owner=configure-system-package-error::"
 
       - name: Build
         shell: bash -l {0}
         run: |
           # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
-          pip install --no-build-isolation --no-deps -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
           pip install --no-build-isolation --no-deps --config-settings editable_mode=compat -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2

diff --git a/.github/workflows/ci-linux.yml b/.github/workflows/ci-linux.yml
@@ -46,7 +46,7 @@ jobs:
       targets: build doc-html
       targets_optional: ptest
       tox_system_factors: >-
-        ["ubuntu-focal"]
+        ["ubuntu-jammy"]
       tox_packages_factors: >-
         ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
@@ -111,18 +111,11 @@ jobs:
         ["ubuntu-jammy",
          "ubuntu-lunar",
          "ubuntu-mantic",
-         "debian-bullseye",
          "debian-bookworm",
          "debian-trixie",
          "debian-sid",
-         "linuxmint-21",
          "linuxmint-21.1",
          "linuxmint-21.2",
-         "fedora-33",
-         "fedora-34",
-         "fedora-35",
-         "fedora-36",
-         "fedora-37",
          "fedora-38",
          "fedora-39",
          "centos-stream-8-python3.9",
@@ -131,11 +124,9 @@ jobs:
          "gentoo-python3.10",
          "gentoo-python3.11",
          "archlinux-latest",
-         "opensuse-15.4-gcc_11-python3.10",
          "opensuse-15.5-gcc_11-python3.11",
          "opensuse-tumbleweed-python3.10",
-         "opensuse-tumbleweed",
-         "debian-bullseye-i386"]
+         "opensuse-tumbleweed"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
       max_parallel: 8
 

diff --git a/.github/workflows/dist.yml b/.github/workflows/dist.yml
@@ -116,7 +116,9 @@ jobs:
           - os: ubuntu-latest
             arch: i686
           - os: macos-latest
-            arch: auto
+            arch: x86_64
+          - os: macos-14
+            arch: arm64
     env:
       # SPKGs to install as system packages
       SPKGS: _bootstrap _prereq
@@ -141,6 +143,14 @@ jobs:
           name: dist
           path: dist
 
+      - 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: Build platform wheels
         # We build the wheels from the sdists so that MANIFEST filtering becomes effective.
         # But we must run cibuildwheel with the unpacked source directory, not a tarball,
@@ -151,12 +161,13 @@ jobs:
         # This is unfortunately repeated for each of the packages that we build wheels for
         # because CIBW starts with a fresh container on each invocation.
         run: |
+          "${{ steps.python.outputs.python-path }}" -m pip install pipx
           export PATH=build/bin:$PATH
           export CIBW_BEFORE_ALL="( $(sage-print-system-package-command debian --yes --no-install-recommends install $(sage-get-system-packages debian $SPKGS)) || $(sage-print-system-package-command fedora --yes --no-install-recommends install $(sage-get-system-packages fedora $SPKGS | sed s/pkg-config/pkgconfig/)) || ( $(sage-print-system-package-command homebrew --yes --no-install-recommends install $(sage-get-system-packages homebrew $SPKGS)) || echo error ignored) ) && ./bootstrap && ./configure --enable-build-as-root && make -j4 V=0 $TARGETS_PRE"
           mkdir -p unpacked
           for pkg in sagemath-objects sagemath-categories; do
               (cd unpacked && tar xfz - ) < dist/$pkg*.tar.gz
-              pipx run cibuildwheel==2.16.2 unpacked/$pkg*
+              "${{ steps.python.outputs.python-path }}" -m pipx run cibuildwheel==2.17.0 unpacked/$pkg*
           done
 
       - uses: actions/upload-artifact@v3