Merge branch 'develop' into develop

Author: PTK12

.github/sync_labels.py

@@ -56,7 +56,7 @@ class ReviewDecision(Enum):
     """
     changes_requested = 'CHANGES_REQUESTED'
     approved = 'APPROVED'
-    unclear = 'COMMENTED'
+    unclear = 'UNCLEAR'
 
 class Priority(Enum):
     r"""
@@ -319,12 +319,15 @@ def get_review_decision(self):
             return None
 
         if self._review_decision is not None:
+            if self._review_decision == ReviewDecision.unclear:
+                return None
             return self._review_decision
 
         data = self.view('reviewDecision')
         if data:
             self._review_decision = ReviewDecision(data)
         else:
+            # To separate a not supplied value from not cached (see https://github.com/sagemath/sage/pull/36177#issuecomment-1704022893 ff)
             self._review_decision = ReviewDecision.unclear
         info('Review decision for %s: %s' % (self._issue, self._review_decision.value))
         return self._review_decision
@@ -349,9 +352,9 @@ def get_reviews(self, complete=False):
             self.get_commits()
 
         date = self._commit_date
-        no_rev = ReviewDecision.unclear.value
+        unproper_rev = RevState.commented.value
         new_revs = [rev for rev in self._reviews if rev['submittedAt'] > date]
-        proper_new_revs = [rev for rev in new_revs if rev['state'] != no_rev]
+        proper_new_revs = [rev for rev in new_revs if rev['state'] != unproper_rev]
         info('Proper reviews after %s for %s: %s' % (date, self._issue, proper_new_revs))
         return proper_new_revs
 
@@ -463,11 +466,6 @@ def approve_allowed(self):
         r"""
         Return if the actor has permission to approve this PR.
         """
-        revs = self.get_reviews(complete=True)
-        if not any(rev['authorAssociation'] in ('MEMBER', 'OWNER') for rev in revs):
-            info('PR %s can\'t be approved because of missing member review' % (self._issue))
-            return False
-
         revs = self.get_reviews()
         revs = [rev for rev in revs if rev['author']['login'] != self._actor]
         ch_req = ReviewDecision.changes_requested

.github/workflows/build.yml

@@ -30,7 +30,7 @@ jobs:
     steps:
       - name: Checkout
         id: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Update system packages
         id: prepare
@@ -103,12 +103,24 @@ jobs:
         run: pyright
         working-directory: ./worktree-image
 
-      - name: Build (fallback to non-incremental)
-        id: build
+      - name: Clean (fallback to non-incremental)
+        id: clean
         if: always() && steps.worktree.outcome == 'success' && steps.incremental.outcome != 'success'
         run: |
           set -ex
-          ./bootstrap && make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage && ./config.status && make build
+          ./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
+
+      - name: Build
+        # This step is needed because building the modularized distributions installs some optional packages,
+        # so the editable install of sagelib needs to build the corresponding optional extension modules.
+        id: build
+        if: always() && (steps.incremental.outcome == 'success' || steps.clean.outcome == 'success')
+        run: |
+          make build
         working-directory: ./worktree-image
         env:
           MAKE: make -j2
@@ -125,22 +137,22 @@ jobs:
           COLUMNS: 120
 
       - name: Test all files (sage -t --all --long)
-        if: always() && (steps.incremental.outcome == 'success' || steps.build.outcome == 'success')
+        if: always() && steps.build.outcome == 'success'
         run: |
           ../sage -python -m pip install coverage
           ../sage -python -m coverage run ./bin/sage-runtests --all --long -p2 --random-seed=286735480429121101562228604801325644303
         working-directory: ./worktree-image/src
 
       - name: Prepare coverage results
-        if: always() && (steps.incremental.outcome == 'success' || steps.build.outcome == 'success')
+        if: always() && steps.build.outcome == 'success'
         run: |
           ./venv/bin/python3 -m coverage combine src/.coverage/
           ./venv/bin/python3 -m coverage xml
           find . -name *coverage*
         working-directory: ./worktree-image
 
       - name: Upload coverage to codecov
-        if: always() && (steps.incremental.outcome == 'success' || steps.build.outcome == 'success')
+        if: always() && steps.build.outcome == 'success'
         uses: codecov/codecov-action@v3
         with:
           files: ./worktree-image/coverage.xml

.github/workflows/ci-conda.yml

@@ -8,6 +8,11 @@ on:
       - 'public/build/**-runci'
   pull_request:
     types:
+      # Defaults
+      - opened
+      - synchronize
+      - reopened
+      # When a CI label is added
       - labeled
   workflow_dispatch:
     # Allow to run manually
@@ -21,13 +26,18 @@ jobs:
   test:
     name: Conda
     runs-on: ${{ matrix.os }}
-    
-    # Run on push, workflow dispatch and when certain labels are added 
+
+    # Run on push, workflow dispatch and when certain labels are added or are present
     if: |
-      github.event.action != 'labeled' ||
-      github.event.label.name == 'c: packages: optional' || 
-      github.event.label.name == 'c: packages: standard' || 
-      github.event.label.name == 's: run conda ci'
+      github.event_name != 'pull_request' ||
+      ((github.event.action != 'labeled' &&
+         (contains(github.event.pull_request.labels.*.name, 'c: packages: standard') ||
+          contains(github.event.pull_request.labels.*.name, 'c: packages: optional') ||
+          contains(github.event.pull_request.labels.*.name, 's: run conda ci'))) ||
+       (github.event.action == 'labeled' &&
+         (github.event.label.name == 'c: packages: optional' ||
+          github.event.label.name == 'c: packages: standard' ||
+          github.event.label.name == 's: run conda ci')))
 
     strategy:
       fail-fast: false
@@ -39,7 +49,7 @@ jobs:
         conda-env: [environment]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check for Miniconda
         id: check_conda

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

@@ -0,0 +1,96 @@
+name: CI Linux incremental
+
+## 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.
+##
+## It builds and checks some sage spkgs as defined in TARGETS.
+##
+## A job succeeds if there is no error.
+##
+## The build is run with "make V=0", so the build logs of individual packages are suppressed.
+##
+## At the end, all package build logs that contain an error are printed out.
+##
+## After all jobs have finished (or are canceled) and a short delay,
+## tar files of all logs are made available as "build artifacts".
+
+on:
+  pull_request:
+    types:
+      # Defaults
+      - opened
+      - synchronize
+      - reopened
+      # When a CI label is added
+      - labeled
+  workflow_dispatch:
+
+concurrency:
+  # Cancel previous runs of this workflow for the same branch
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  packages: write
+
+jobs:
+
+  changed_files:
+    runs-on: ubuntu-latest
+    name: List changed packages
+    outputs:
+      uninstall_targets: ${{ steps.build-targets.outputs.uninstall_targets }}
+      build_targets:     ${{ steps.build-targets.outputs.build_targets }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get all packages that have changed
+        id: changed-packages
+        uses: tj-actions/changed-files@v38
+        with:
+          files_yaml: |
+            configures:
+              - 'build/pkgs/*/spkg-configure.m4'
+            pkgs:
+              - 'build/pkgs/**'
+              - 'pkgs/**'
+      - name: Determine targets to build
+        id: build-targets
+        run: |
+          echo "uninstall_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))" >> $GITHUB_OUTPUT
+          echo "build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([-_.a-z0-9]*)/[^ ]* *,\2-ensure,;'; done | sort -u))" >> $GITHUB_OUTPUT
+          cat $GITHUB_OUTPUT
+  minimal:
+    needs: [changed_files]
+    if: |
+      github.event_name != 'pull_request' ||
+      ((github.event.action != 'labeled' &&
+         (contains(github.event.pull_request.labels.*.name, 'c: packages: standard') ||
+          contains(github.event.pull_request.labels.*.name, 'c: packages: optional'))) ||
+       (github.event.action == 'labeled' &&
+         (github.event.label.name == 'c: packages: optional' ||
+          github.event.label.name == 'c: packages: standard')))
+    uses: ./.github/workflows/docker.yml
+    with:
+      # Build incrementally from published Docker image
+      incremental: true
+      free_disk_space: true
+      from_docker_repository: ghcr.io/sagemath/sage/
+      from_docker_target: "with-targets"
+      from_docker_tag: "dev"
+      docker_targets: "with-targets"
+      targets: "${{needs.changed_files.outputs.uninstall_targets}} ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      tox_system_factors: >-
+        ["ubuntu-focal",
+         "ubuntu-jammy",
+         "ubuntu-mantic",
+         "debian-bullseye",
+         "debian-bookworm",
+         "fedora-30",
+         "fedora-38",
+         "gentoo-python3.11",
+         "debian-bullseye-i386"]
+      tox_packages_factors: >-
+          ["standard",
+           "minimal"]
+      docker_push_repository: ghcr.io/${{ github.repository }}/

.github/workflows/ci-linux.yml

@@ -63,6 +63,56 @@ jobs:
           ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
 
+  standard-sitepackages:
+    if: ${{ success() || failure() }}
+    needs: [standard-pre]
+    uses: ./.github/workflows/docker.yml
+    with:
+      # Build incrementally from previous stage (pre)
+      incremental: true
+      free_disk_space: true
+      from_docker_repository: ghcr.io/${{ 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-kinetic",
+         "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",
+         "centos-stream-9-python3.9",
+         "almalinux-8-python3.9",
+         "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"]
+      docker_push_repository: ghcr.io/${{ github.repository }}/
+      max_parallel: 10
+
   minimal-pre:
     if: ${{ success() || failure() }}
     # It does not really "need" it.

.github/workflows/ci-macos.yml

@@ -47,7 +47,7 @@ jobs:
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-tox-local-${{ matrix.tox_env }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_env }}--${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Select Xcode version
         run: |
           if [ ${{ matrix.xcode_version_factor }} != default ]; then sudo xcode-select -s /Applications/Xcode_${{ matrix.xcode_version_factor }}.app; fi
@@ -118,7 +118,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 500
       - name: fetch tags
@@ -160,7 +160,7 @@ jobs:
       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@v3
+      - uses: actions/checkout@v4
         if: "!contains(matrix.tox_system_factor, 'nobootstrap')"
       - uses: actions/download-artifact@v3
         with:

.github/workflows/ci-wsl.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
     - name: Configure git
       run: git config --global core.symlinks true
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Ubuntu 20.04 (in WSL)
       run: |
         (New-Object System.Net.WebClient).DownloadFile("https://aka.ms/wslubuntu2004", "Ubuntu.appx")

.github/workflows/cygwin.yml

@@ -73,14 +73,14 @@ jobs:
         choco install git python39 python39-pip --source cygwin
 
     - name: Check out SageMath
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: ${{ inputs.sage_repo }}
         ref: ${{ inputs.sage_ref }}
         fetch-depth: 2000
 
     - name: Check out git-trac-command
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: sagemath/git-trac-command
         path: git-trac-command

.github/workflows/dist.yml

@@ -32,7 +32,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install bootstrap prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
@@ -51,7 +51,7 @@ jobs:
     env:
       CAN_DEPLOY: ${{ secrets.SAGEMATH_PYPI_API_TOKEN != '' }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install bootstrap prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
@@ -100,13 +100,13 @@ jobs:
       #
       CIBW_ARCHS: ${{ matrix.arch }}
       # https://cibuildwheel.readthedocs.io/en/stable/options/#requires-python
-      CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+      CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
       # Environment during wheel build
       CIBW_ENVIRONMENT: "PATH=$(pwd)/local/bin:$PATH CPATH=$(pwd)/local/include:$CPATH LIBRARY_PATH=$(pwd)/local/lib:$LIBRARY_PATH PKG_CONFIG_PATH=$(pwd)/local/share/pkgconfig:$PKG_CONFIG_PATH ACLOCAL_PATH=/usr/share/aclocal"
       # Use 'build', not 'pip wheel'
       CIBW_BUILD_FRONTEND: build
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/download-artifact@v3
         with: