Merge tag '10.3.beta5' into public/ideals_for_non_maximal_orders

SageMath version 10.3.beta5, Release Date: 2024-01-14

.devcontainer/devcontainer.json

@@ -8,7 +8,7 @@
 	"remoteUser": "vscode",
 
 	// Setup conda environment
-	"onCreateCommand": ".devcontainer/onCreate-conda.sh",
+	"onCreateCommand": ".devcontainer/onCreate-conda.sh || true",
 
 	// Install additional features.
 	"features": {

.devcontainer/downstream-archlinux-latest/devcontainer.json

@@ -3,7 +3,7 @@
     "name": "archlinux:latest downstream Sage",
     "image": "archlinux:latest",
     // Create an empty bashrc to avoid the error "No such file or directory" when opening a terminal.
-    "onCreateCommand": "EXTRA_SYSTEM_PACKAGES='sagemath sagemath-doc' EXTRA_SAGE_PACKAGES='notebook pip' .devcontainer/onCreate.sh && touch ~/.bashrc",
+    "onCreateCommand": "sed -i '/^NoExtract/d' /etc/pacman.conf; EXTRA_SYSTEM_PACKAGES='sagemath sagemath-doc' EXTRA_SAGE_PACKAGES='notebook pip' .devcontainer/onCreate.sh && touch ~/.bashrc",
     // There's no SAGE_LOCAL, so remove the symlink 'prefix'.
     "updateContentCommand": "rm -f prefix && ln -sf /usr venv",
     "extensions": [

.devcontainer/onCreate-conda.sh

@@ -2,9 +2,8 @@
 set -e
 
 # Create conda environment
-./bootstrap-conda
 conda install mamba -n base -c conda-forge -y
-mamba env create --file src/environment-dev-3.11.yml || mamba env update --file src/environment-dev-3.11.yml
+mamba env create --file src/environment-dev-3.11-linux.yml || mamba env update --file src/environment-dev-3.11-linux.yml
 conda init bash
 
 # Build sage

.github/workflows/build.yml

@@ -172,11 +172,23 @@ jobs:
           MAKE: make -j2 --output-sync=recurse
           SAGE_NUM_THREADS: 2
 
+      - name: Check that all modules can be imported
+        run: |
+          # The following command checks that all modules can be imported.
+          # The output also includes a long list of modules together with the number of tests in each module.
+          # This can be ignored.
+          ../sage -python -m pip install pytest-xdist
+          ../sage -python -m pytest -c tox.ini -qq --doctest --collect-only || true
+        working-directory: ./worktree-image/src
+        env:
+          # Increase the length of the lines in the "short summary"
+          COLUMNS: 120
+
       - name: Pytest
         if: contains(github.ref, 'pytest')
         run: |
           ../sage -python -m pip install coverage pytest-xdist
-          ../sage -python -m coverage run -m pytest -c tox.ini --doctest-modules || true
+          ../sage -python -m coverage run -m pytest -c tox.ini --doctest || true
         working-directory: ./worktree-image/src
         env:
           # Increase the length of the lines in the "short summary"

.github/workflows/ci-conda.yml

@@ -18,11 +18,11 @@ concurrency:
 jobs:
   test:
     name: Conda
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
 
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu, macos]
         python: ['3.9', '3.10', '3.11']
         # Optional environment is disabled for now as its not yet working
         # environment: [environment, environment-optional]
@@ -38,9 +38,6 @@ jobs:
           GH_TOKEN: ${{ github.token }}
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
 
-      - name: Create conda environment files
-        run: ./bootstrap-conda
-
       - name: Cache conda packages
         uses: actions/cache@v3
         with:
@@ -57,7 +54,7 @@ jobs:
           channels: conda-forge
           channel-priority: true
           activate-environment: sage
-          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}.yml
+          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && 'macos' || 'linux' }}.yml
 
       - name: Print Conda environment
         shell: bash -l {0}

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

@@ -63,6 +63,21 @@ jobs:
           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][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))" >> $GITHUB_OUTPUT
           echo "build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))" >> $GITHUB_OUTPUT
           cat $GITHUB_OUTPUT
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.base_ref }}
+          path: worktree-base
+        if: github.base_ref
+      - name: Compute metrics
+        run: |
+          export PATH=build/bin:$PATH
+          if [ -d worktree-base ]; then
+            (echo "# $GITHUB_BASE_REF"; SAGE_ROOT=worktree-base sage-package metrics :all:) > base-metrics.txt
+            (echo "# $GITHUB_REF"; sage-package metrics :all:) > metrics.txt
+            diff --color=always --width=100 --side-by-side --left-column base-metrics.txt metrics.txt || true
+          else
+            sage-package metrics :all:
+          fi
 
   test:
     needs: [changed_files]
@@ -83,7 +98,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
       tox_system_factors: >-
         ["ubuntu-focal",
          "ubuntu-jammy",
@@ -119,7 +134,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
       # 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: >-

.github/workflows/conda-lock-update.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+
+from pathlib import Path
+import subprocess
+
+script_dir = Path(__file__).resolve().parent
+root_dir = script_dir / '..' / '..'
+
+subprocess.run([str(root_dir / "bootstrap-conda")])
+
+platforms = {
+    "linux-64": "linux",
+    "linux-aarch64": "linux-aarch64",
+    "osx-64": "macos",
+    "osx-arm64": "macos-arm64"
+    #"win-64": "win",
+}
+pythons = ["3.9", "3.10", "3.11"]
+tags = ["", "-dev"]
+sources = ["", "src"]
+
+for platform_key, platform_value in platforms.items():
+    for python in pythons:
+        for tag in tags:
+            for src in sources:
+                env_file = root_dir / src / f"environment{tag}-{python}.yml"
+                lock_file = root_dir / src / f"environment{tag}-{python}-{platform_value}"
+
+                if not env_file.exists():
+                    continue
+
+                print(f"Updating lock file for {env_file} at {lock_file}", flush=True)
+                subprocess.run(["conda-lock", "--channel", "conda-forge", "--kind", "env", "--platform", platform_key, "--file", str(env_file), "--lockfile", str(lock_file), "--filename-template", str(lock_file)])

.gitpod.yml

@@ -7,8 +7,7 @@ tasks:
   - name: Setup
     # Create conda environment, then configure and build sage
     init: >-
-      ./bootstrap-conda
-      && mamba env create --file src/environment-dev-3.11.yml --prefix venv
+      && mamba env create --file src/environment-dev-3.11-linux.yml --prefix venv
       && conda config --append envs_dirs $(pwd)
       && conda activate $(pwd)/venv
       && ./bootstrap

.vscode/launch.json

@@ -1,6 +1,20 @@
 {
     "version": "0.2.0",
     "configurations": [
+        {
+            "name": "Sage: Pytest Doctests",
+            "type": "python",
+            "request": "launch",
+            "module": "pytest",
+            "args": [
+                "-c",
+                "src/tox.ini",
+                "--doctest",
+                "${file}"
+            ],
+            "console": "integratedTerminal",
+            "justMyCode": false
+        },
         {
             "name": "Sage: Pytest",
             "type": "python",
@@ -33,4 +47,4 @@
             "justMyCode": false
         }
     ],
-}
+}

.vscode/settings.json

@@ -35,5 +35,6 @@
         "sagemath",
         "Cython"
     ],
-    "editor.formatOnType": true
+    "editor.formatOnType": true,
+    "esbonio.sphinx.confDir": ""
 }

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.3.beta4
+version: 10.3.beta5
 doi: 10.5281/zenodo.593563
-date-released: 2023-12-26
+date-released: 2024-01-14
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

Makefile

@@ -50,6 +50,9 @@ SPKG_COLLECT_FILES = build/pkgs/*/type build/pkgs/*/package-version.txt build/pk
 # If configure was run before, rerun it with the old arguments.
 # Otherwise, run configure with argument $PREREQ_OPTIONS.
 build/make/Makefile: configure $(SPKG_COLLECT_FILES) $(CONFIG_FILES:%=%.in)
+	$(MAKE) reconfigure
+
+reconfigure:
 	rm -f config.log
 	mkdir -p logs/pkgs
 	ln -s logs/pkgs/config.log config.log
@@ -339,7 +342,7 @@ list:
 	@$(MAKE) --silent build/make/Makefile >&2
 	@$(MAKE) --silent -f build/make/Makefile SAGE_PKGCONFIG=dummy $@
 
-.PHONY: default build dist install micro_release \
+.PHONY: default build dist install micro_release reconfigure \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.3.beta4, Release Date: 2023-12-26
+SageMath version 10.3.beta5, Release Date: 2024-01-14

bootstrap

@@ -108,8 +108,8 @@ EOF
             if test -f "$DIR/requirements.txt" -o -f "$DIR/install-requires.txt"; then
                 # A Python package
                 SPKG_TREE_VAR=SAGE_VENV
-                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(ENABLE_SYSTEM_SITE_PACKAGES=yes sage-get-system-packages install-requires ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions.m4
-                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(ENABLE_SYSTEM_SITE_PACKAGES=yes sage-get-system-packages install-requires-toml ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions_toml.m4
+                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(sage-get-system-packages install-requires ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions.m4
+                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(sage-get-system-packages install-requires-toml ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions_toml.m4
             fi
         fi
         spkg_finalizes="$spkg_finalizes

bootstrap-conda

@@ -115,6 +115,7 @@ echo >&2 $0:$LINENO: generate conda environment files
     (
         sed 's/name: sage/name: sage-dev/' src/environment-template.yml
         echo "  # Additional dev tools"
+        echo "  - conda-lock"
         for pkg in $DEVELOP_SYSTEM_PACKAGES; do
             echo "  - $pkg"
         done

build/bin/sage-get-system-packages

@@ -47,16 +47,28 @@ case "$SYSTEM" in
 esac
 for PKG_BASE in $SPKGS; do
 
-    # Skip this package if it uses the SAGE_PYTHON_PACKAGE_CHECK
-    # macro and if --enable-system-site-packages was NOT passed
-    # to ./configure (or if ./configure has not yet been run).
-    SPKG_CONFIGURE="${SAGE_ROOT}/build/pkgs/${PKG_BASE}/spkg-configure.m4"
-    if [ -z "${ENABLE_SYSTEM_SITE_PACKAGES}" ]; then
-        if grep -q SAGE_PYTHON_PACKAGE_CHECK "${SPKG_CONFIGURE}" 2>/dev/null;
-        then
-            continue;
-        fi
-    fi
+    case "$SYSTEM:$ENABLE_SYSTEM_SITE_PACKAGES" in
+        install-requires*|pip*)
+            # This is output for installation of packages into a Python environment.
+            # So it's OK to use any Python packages.
+            ;;
+        *:)
+            # --enable-system-site-packages was NOT passed to configure
+            # (or script was run outside of the sage-build-env).
+            #
+            # Skip this package if it uses the SAGE_PYTHON_PACKAGE_CHECK macro.
+            #
+            SPKG_CONFIGURE="${SAGE_ROOT}/build/pkgs/${PKG_BASE}/spkg-configure.m4"
+            if grep -q SAGE_PYTHON_PACKAGE_CHECK "${SPKG_CONFIGURE}" 2>/dev/null;
+            then
+                continue
+            fi
+            ;;
+        *)
+            # --enable-system-site-packages was passed to configure.
+            # So any package (Python, non-Python) is fine.
+            ;;
+    esac
 
     for NAME in $SYSTEM_PACKAGES_FILE_NAMES; do
         SYSTEM_PACKAGES_FILE="$SAGE_ROOT"/build/pkgs/$PKG_BASE/$NAME

build/bin/write-dockerfile.sh

@@ -128,9 +128,8 @@ EOF
         ENDRUN=\'
         ;;
     void*)
-	# https://hub.docker.com/r/voidlinux/masterdir-x86_64-musl
-        UPDATE="xbps-install -Su &&"
-        EXISTS="xbps-query"
+        UPDATE="xbps-install -Suy &&"
+        EXISTS="xbps-query -R"
         INSTALL="xbps-install --yes"
         ;;
     opensuse*)

build/pkgs/_prereq/distros/void.txt

@@ -16,4 +16,19 @@ make
 perl
 python3
 tar
+bash
 which
+# needed by gfortran
+diffutils
+# needed by ppl
+gzip
+# void may need special patches for musl libc support in python3,
+# so require full python 3 and its prereqs
+python3-devel
+bzip2-devel
+xz
+liblzma-devel
+libffi-devel
+zlib-devel
+# to build python3 with the crypto module; there may be other packages that need it
+libxcrypt-devel

build/pkgs/_python3.11/distros/void.txt

@@ -0,0 +1 @@
+python3.11-devel

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=05115739db242cb5a48ae17f97d06b179fc70334
-md5=adc8208885e6be527b089b682079c464
-cksum=3321256447
+sha1=1041fee1d3ed5dc9c6c428668a895fb7109a48e5
+md5=e254e55345074cd0959cb21c8e4716ca
+cksum=1271538328

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-e95536ccbad199de456e804968a775f2744e4bff
+c6bf497a0fd0f29c721481b52afaf49969c0cef8

build/pkgs/cython/checksums.ini

@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=94945822403911b75608fa9689039187686437dd
-md5=3b08e76d112619ed9b5bc240b6b53cf4
-cksum=467020180
+sha1=48f0535ce0b05e0e4ae4daa6a597a2cdd76274f5
+md5=94ab8466d9350a31cfef3a0853c2fea5
+cksum=2507297160
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-3.0.6
+3.0.7