Merge branch 'develop' into bliss_spkg_config

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -3,33 +3,11 @@ description: Report a bug
 title: "<title>"
 labels: "t: bug"
 body:
-  - type: checkboxes
-    attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
-  - type: checkboxes
-    attributes:
-      label: Did you read the documentation and troubleshoot guide?
-      description: Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
-      options:
-      - label: I have read the documentation and troubleshoot guide
-        required: true
-  - type: textarea
+  - type: markdown
     attributes:
-      label: Environment
-      description: |
-        examples:
-          - **OS**: Ubuntu 20.04
-          - Sage Version: 9.2
       value: |
-          - **OS**:
-          - **Sage Version**: 
-      render: markdown
-    validations:
-      required: true
+        * Please search to see if an issue already exists for the bug you encountered.
+        * Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
   - type: textarea
     attributes:
       label: Steps To Reproduce
@@ -60,3 +38,24 @@ body:
         Links? References? Anything that will give us more context about the issue you are encountering!
     validations:
       required: false
+  - type: textarea
+    attributes:
+      label: Environment
+      description: |
+        examples:
+          - **OS**: Ubuntu 20.04
+          - Sage Version: 9.2
+      value: |
+          - **OS**:
+          - **Sage Version**:
+      render: markdown
+    validations:
+      required: true
+  - type: checkboxes
+    attributes:
+      label: Checklist
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true
+      - label: I have read the documentation and troubleshoot guide
+        required: true

.github/ISSUE_TEMPLATE/failure_building_from_source.yml

@@ -4,20 +4,11 @@ title: "<title>"
 labels: ['c: build', 't: bug']
 assignees: []
 body:
-  - type: checkboxes
+  - type: markdown
     attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
-  - type: checkboxes
-    attributes:
-      label: Did you read the documentation and troubleshoot guide?
-      description: Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting sectionin the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
-      options:
-      - label: I have read the documentation and troubleshoot guide
-        required: true
+      value: |
+        * Please search to see if an issue already exists for the bug you encountered.
+        * Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
   - type: textarea
     attributes:
       label: Environment
@@ -65,3 +56,11 @@ body:
         Links? References? Anything that will give us more context about the issue you are encountering!
     validations:
       required: false
+  - type: checkboxes
+    attributes:
+      label: Checklist
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true
+      - label: I have read the documentation and troubleshoot guide
+        required: true

.github/ISSUE_TEMPLATE/feature_report.yml

@@ -3,13 +3,10 @@ description: Suggest an idea
 title: "<title>"
 labels: "t: enhancement"
 body:
-  - type: checkboxes
+  - type: markdown
     attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
+      value: |
+        * Please search to see if an issue already exists for the bug you encountered.
   - type: textarea
     attributes:
       label: Problem Description
@@ -34,3 +31,9 @@ body:
       description: Add any other context about the problem here.
     validations:
       required: false
+  - type: checkboxes
+    attributes:
+      label: Is there an existing issue for this?
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,17 +1,20 @@
-<!-- Please provide a concise, informative and self-explanatory title. -->
-<!-- Don't put issue numbers in the title. Put it in the Description below. -->
-<!-- For example, instead of "Fixes #12345", use "Add a new method to multiply two integers" -->
-
-### :books: Description
+<!-- ^^^^^
+Please provide a concise, informative and self-explanatory title.
+Don't put issue numbers in there, do this in the PR body below.
+For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1"
+-->
+<!-- Describe your changes here in detail -->
 
-<!-- Describe your changes here in detail. -->
 <!-- Why is this change required? What problem does it solve? -->
 <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". -->
 <!-- If your change requires a documentation PR, please link it appropriately. -->
 
 ### :memo: Checklist
 
-<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x ]`. -->
+<!-- Put an `x` in all the boxes that apply. -->
+<!-- If your change requires a documentation PR, please link it appropriately -->
+<!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+<!-- Feel free to remove irrelevant items. -->
 
 - [ ] The title is concise, informative, and self-explanatory.
 - [ ] The description explains in detail what this PR is about.

.github/workflows/build.yml

@@ -60,11 +60,13 @@ jobs:
           # (This keeps mtimes of unchanged files unchanged and mtimes of changed files newer than unchanged files.)
           # Finally we reset the index to "old". (This keeps all mtimes unchanged.)
           # The changed files now show up as uncommitted changes.
+          # The final "git add -N" makes sure that files that were added in "new" do not show
+          # as untracked files, which would be removed by "git clean -fx".
           git worktree add --detach worktree-image
           rm -rf /sage/.git && mv worktree-image/.git /sage/
           rm -rf worktree-image && ln -s /sage worktree-image
           if [ ! -f worktree-image/.gitignore ]; then cp .gitignore worktree-image/; fi
-          (cd worktree-image && git add -A && git commit --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset old)
+          (cd worktree-image && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset --quiet old && git add -N . && git status)
 
       - name: Incremental build, test changed files (sage -t --new)
         id: incremental
@@ -101,12 +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
@@ -123,22 +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

@@ -34,7 +34,9 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python: ['3.9', '3.10', '3.11']
-        conda-env: [environment, environment-optional]
+        # Optional environment is disabled for now as its not yet working
+        # environment: [environment, environment-optional]
+        conda-env: [environment]
 
     steps:
       - uses: actions/checkout@v3
@@ -100,19 +102,20 @@ jobs:
           SAGE_NUM_THREADS: 2
 
       - name: Verify dependencies
-        if: always()
+        if: success() || failure()
         shell: bash -l {0}
         run: pip check
 
       - name: Test
+        if: success() || failure()
         shell: bash -l {0}
         run: ./sage -t --all -p0
 
       - name: Print logs
+        if: always()
         run: |
           for file in $(find . -type f -name "*.log"); do
               echo "::group::$file"
               cat "$file"
               echo "::endgroup::"
           done
-        if: always()

.github/workflows/dist.yml

@@ -100,7 +100,7 @@ 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'

.github/workflows/doc-build.yml

@@ -44,13 +44,15 @@ jobs:
           # (This keeps mtimes of unchanged files unchanged and mtimes of changed files newer than unchanged files.)
           # Finally we reset the index to "old". (This keeps all mtimes unchanged.)
           # The changed files now show up as uncommitted changes.
+          # The final "git add -N" makes sure that files that were added in "new" do not show
+          # as untracked files, which would be removed by "git clean -fx".
           git worktree add --detach worktree-image
           rm -rf /sage/.git && mv worktree-image/.git /sage/
           rm -rf worktree-image && ln -s /sage worktree-image
           if [ ! -f worktree-image/.gitignore ]; then cp .gitignore worktree-image/; fi
-          (cd worktree-image && git add -A && git commit --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset old)
+          (cd worktree-image && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset --quiet old && git add -N . && git status)
           # Keep track of changes to built HTML
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git init && (echo ".buildinfo"; echo ".inv") > .gitignore; git add -A && git commit --quiet -m "old")
+          new_version=$(cat src/VERSION.txt); (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage '$new_version' /'; git init && (echo "*.svg binary"; echo "*.pdf binary") >> .gitattributes && (echo ".buildinfo"; echo '*.inv'; echo '.git*'; echo '*.svg'; echo '*.pdf'; echo '*.png'; echo 'searchindex.js') > .gitignore; git add -A && git commit --quiet -m "old")
 
       - name: Incremental build
         id: incremental
@@ -80,7 +82,10 @@ jobs:
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |
           set -ex
-          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage && ./config.status && make doc-html
+          mv /sage/local/share/doc/sage/html/en/.git /sage/.git-doc
+          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage
+          mkdir -p /sage/local/share/doc/sage/html/en/ && mv /sage/.git-doc /sage/local/share/doc/sage/html/en/.git
+          ./config.status && make doc-html
         working-directory: ./worktree-image
         env:
           MAKE: make -j2
@@ -94,7 +99,7 @@ jobs:
           mkdir -p ./docs
           # Create changelog
           echo '## Preview of CHANGES.html'
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git diff --name-only) | tee ./docs/CHANGES.txt
+          (cd /sage/local/share/doc/sage/html/en && git diff --name-only) | tee ./docs/CHANGES.txt
           (cd /sage/local/share/doc/sage/html/en && git diff; rm -rf .git) > ./docs/html.diff
           echo '## Preview of html.diff'; head -n 400 ./docs/html.diff
           (echo '<p><a href="html.diff">HTML diff</a>'; sed -E 's,(.*),<p><a href="\1">\1</a>,' ./docs/CHANGES.txt) > ./docs/CHANGES.html

.github/workflows/docker.yml

@@ -18,26 +18,23 @@ on:
         default: >-
           ["ubuntu-trusty-toolchain-gcc_9",
            "ubuntu-xenial-toolchain-gcc_9",
-           "ubuntu-bionic-gcc_8-python3.8",
            "ubuntu-focal",
            "ubuntu-jammy",
            "ubuntu-kinetic",
            "ubuntu-lunar",
            "ubuntu-mantic",
-           "debian-buster",
+           "debian-buster-gcc_spkg",
            "debian-bullseye",
            "debian-bookworm",
+           "debian-trixie",
            "debian-sid",
-           "linuxmint-19-gcc_8-python3.8",
-           "linuxmint-19.3-gcc_8-python3.8",
            "linuxmint-20.1",
            "linuxmint-20.2",
            "linuxmint-20.3",
            "linuxmint-21",
            "linuxmint-21.1",
            "linuxmint-21.2",
-           "fedora-29-python3.8",
-           "fedora-30-python3.8",
+           "fedora-30",
            "fedora-31",
            "fedora-32",
            "fedora-33",
@@ -50,6 +47,8 @@ on:
            "centos-7-devtoolset-gcc_11",
            "centos-stream-8-python3.9",
            "centos-stream-9-python3.9",
+           "almalinux-8-python3.9",
+           "almalinux-9-python3.11",
            "gentoo-python3.10",
            "gentoo-python3.11",
            "archlinux-latest",
@@ -59,7 +58,6 @@ on:
            "opensuse-tumbleweed-python3.10",
            "conda-forge",
            "ubuntu-bionic-gcc_8-i386",
-           "debian-buster-i386",
            "debian-bullseye-i386",
            ]
       tox_packages_factors:

.github/workflows/lint.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install pycodestyle
       run: pip install tox pycodestyle
     - name: Lint using pycodestyle
@@ -31,7 +31,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install relint
       run: pip install tox relint
     - name: Lint using relint
@@ -45,7 +45,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install tox
       run: pip install tox
     - name: Lint using tox -e rst