Merge branch 'develop' into combinat/signed_perm_cycles

Author: tscrim

.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

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

@@ -0,0 +1,97 @@
+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:     ${{ steps.build-targets.outputs.build_targets }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Get all packages that have changed
+        id: changed-packages
+        uses: tj-actions/changed-files@v38
+        with:
+          files_yaml: |
+            configures:
+              - 'build/pkgs/*/spkg-configure.m4'
+            pkgs:
+              - 'build/pkgs/**'
+              - 'pkgs/**'
+      - name: Determine targets to build
+        id: build-targets
+        run: |
+          echo "uninstall_targets=$(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}} ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      tox_system_factors: >-
+        ["ubuntu-focal",
+         "ubuntu-jammy",
+         "ubuntu-mantic,
+         "debian-bullseye",
+         "debian-bookworm",
+         "ubuntu-mantic,
+         "fedora-30",
+         "fedora-38",
+         "gentoo-python3.11",
+         "debian-bullseye-i386"]
+      tox_packages_factors: >-
+          ["standard",
+           "minimal"]
+      docker_push_repository: ghcr.io/${{ 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/docker.yml

@@ -18,6 +18,7 @@ on:
         default: >-
           ["ubuntu-trusty-toolchain-gcc_9",
            "ubuntu-xenial-toolchain-gcc_9",
+           "ubuntu-bionic-gcc_8",
            "ubuntu-focal",
            "ubuntu-jammy",
            "ubuntu-kinetic",
@@ -56,6 +57,7 @@ on:
            "opensuse-15.4-gcc_11-python3.10",
            "opensuse-15.5-gcc_11-python3.11",
            "opensuse-tumbleweed-python3.10",
+           "opensuse-tumbleweed",
            "conda-forge",
            "ubuntu-bionic-gcc_8-i386",
            "debian-bullseye-i386",

.vscode/settings.json

@@ -27,7 +27,7 @@
     "python.linting.enabled": true,
     // The following pycodestyle arguments are the same as the pycodestyle-minimal
     // tox environnment, see the file SAGE_ROOT/src/tox.ini
-    "python.linting.pycodestyleArgs": ["--select= E111,E21,E222,E227,E25,E271,E303,E306,E401,E502,E701,E702,E703,E71,E72,W291,W293,W391,W605"],
+    "python.linting.pycodestyleArgs": ["--select= E111,E21,E222,E227,E25,E271,E303,E305,E306,E401,E502,E701,E702,E703,E71,E72,W291,W293,W391,W605"],
     "cSpell.words": [
         "furo",
         "Conda",

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.2.beta1
+version: 10.2.beta2
 doi: 10.5281/zenodo.593563
-date-released: 2023-09-01
+date-released: 2023-09-10
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.2.beta1, Release Date: 2023-09-01
+SageMath version 10.2.beta2, Release Date: 2023-09-10

build/bin/sage-build-env-config.in

@@ -53,9 +53,13 @@ export SAGE_PARI_CFG="@SAGE_PARI_CFG@"
 
 export SAGE_GLPK_PREFIX="@SAGE_GLPK_PREFIX@"
 export SAGE_FREETYPE_PREFIX="@SAGE_FREETYPE_PREFIX@"
+export SAGE_PIP_INSTALL_FLAGS="@SAGE_PIP_INSTALL_FLAGS@"
 export SAGE_SUITESPARSE_PREFIX="@SAGE_SUITESPARSE_PREFIX@"
 
 export SAGE_CONFIGURE_FFLAS_FFPACK="@SAGE_CONFIGURE_FFLAS_FFPACK@"
 
 export CONFIGURED_SAGE_EDITABLE="@SAGE_EDITABLE@"
 export CONFIGURED_SAGE_WHEELS="@SAGE_WHEELS@"
+
+export ENABLE_SYSTEM_SITE_PACKAGES="@ENABLE_SYSTEM_SITE_PACKAGES@"
+export PYTHON_MINOR="@PYTHON_MINOR@"

build/bin/sage-dist-helpers

@@ -325,7 +325,11 @@ sdh_store_wheel() {
 }
 
 sdh_store_and_pip_install_wheel() {
-    local pip_options=""
+    # The $SAGE_PIP_INSTALL_FLAGS variable is set by sage-build-env-config.
+    # We skip sanity checking its contents since you should either let sage
+    # decide what it contains, or really know what you are doing.
+    local pip_options="${SAGE_PIP_INSTALL_FLAGS}"
+
     while [ $# -gt 0 ]; do
         case $1 in
             -*) pip_options="$pip_options $1"

build/bin/sage-get-system-packages

@@ -1,4 +1,5 @@
 #!/bin/sh
+
 SYSTEM=$1
 if [ -z "$SYSTEM" ]; then
    echo >&2 "usage: $0 {auto|debian|arch|conda|pip|...} SPKGS..."
@@ -10,6 +11,7 @@ SPKGS="$*"
 if [ -z "$SAGE_ROOT" ]; then
     SAGE_ROOT=`pwd`
 fi
+
 case "$SYSTEM" in
     install-requires)
         # Collect install-requires.txt (falling back to requirements.txt) and output it in the format
@@ -44,6 +46,18 @@ 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
+
     for NAME in $SYSTEM_PACKAGES_FILE_NAMES; do
         SYSTEM_PACKAGES_FILE="$SAGE_ROOT"/build/pkgs/$PKG_BASE/$NAME
         if [ -f $SYSTEM_PACKAGES_FILE ]; then

build/bin/sage-spkg-info

@@ -110,17 +110,19 @@ if [ -z "$system" ]; then
     echo "(none known)"
 else
     echo
-    if [ -f "$PKG_SCRIPTS"/spkg-configure.m4 ]; then
-        echo "If the system package is installed, ./configure will check whether it can be used."
-    else
-        echo "However, these system packages will not be used for building Sage"
-        if [ -f "$PKG_SCRIPTS"/install-requires.txt ]; then
-            echo "because using Python site-packages is not supported by the Sage distribution;"
-            echo "see https://github.com/sagemath/sage/issues/29023"
+    SPKG_CONFIGURE="${PKG_SCRIPTS}/spkg-configure.m4"
+    if [ -f "${SPKG_CONFIGURE}" ]; then
+        if grep -q SAGE_PYTHON_PACKAGE_CHECK "${SPKG_CONFIGURE}"; then
+            echo "If the system package is installed and if the (experimental) option"
+            echo "--enable-system-site-packages is passed to ./configure, then ./configure"
+            echo "will check if the system package can be used."
         else
-            echo "because spkg-configure.m4 has not been written for this package;"
-            echo "see https://github.com/sagemath/sage/issues/27330"
+            echo "If the system package is installed, ./configure will check if it can be used."
         fi
+    else
+        echo "However, these system packages will not be used for building Sage"
+        echo "because spkg-configure.m4 has not been written for this package;"
+        echo "see https://github.com/sagemath/sage/issues/27330"
     fi
 fi
 echo

build/bin/write-dockerfile.sh

@@ -5,7 +5,7 @@
 set -e
 SYSTEM="${1:-debian}"
 shopt -s extglob
-SAGE_PACKAGE_LIST_ARGS="${2:- --has-file=spkg-configure.m4 :standard:}"
+SAGE_PACKAGE_LIST_ARGS="${2:-:standard:}"
 WITH_SYSTEM_SPKG="${3:-yes}"
 IGNORE_MISSING_SYSTEM_PACKAGES="${4:-no}"
 EXTRA_SAGE_PACKAGES="${5:-_bootstrap}"
@@ -15,17 +15,13 @@ SAGE_ROOT=.
 export PATH="$SAGE_ROOT"/build/bin:$PATH
 SYSTEM_PACKAGES=$EXTRA_SYSTEM_PACKAGES
 CONFIGURE_ARGS="--enable-option-checking "
-for PKG_BASE in $(sage-package list --has-file=distros/$SYSTEM.txt $SAGE_PACKAGE_LIST_ARGS) $EXTRA_SAGE_PACKAGES; do
-    PKG_SCRIPTS="$SAGE_ROOT"/build/pkgs/$PKG_BASE
-    if [ -d $PKG_SCRIPTS ]; then
-       SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/$SYSTEM.txt
-       PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
-       if [ -n "PKG_SYSTEM_PACKAGES" ]; then
-           SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
-           if [ -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
-               CONFIGURE_ARGS+="--with-system-$PKG_BASE=${WITH_SYSTEM_SPKG} "
-           fi
-       fi
+for SPKG in $(sage-package list --has-file=spkg-configure.m4 $SAGE_PACKAGE_LIST_ARGS) $EXTRA_SAGE_PACKAGES; do
+    SYSTEM_PACKAGE=$(sage-get-system-packages $SYSTEM $SPKG | sed 's/${PYTHON_MINOR}/'${PYTHON_MINOR}'/g')
+    if [ -n "${SYSTEM_PACKAGE}" ]; then
+	# SYSTEM_PACKAGE can be empty if, for example, the environment
+	# variable ENABLE_SYSTEM_SITE_PACKAGES is empty.
+	SYSTEM_PACKAGES+=" ${SYSTEM_PACKAGE}"
+	CONFIGURE_ARGS+="--with-system-${SPKG}=${WITH_SYSTEM_SPKG} "
     fi
 done
 echo "# Automatically generated by SAGE_ROOT/build/bin/write-dockerfile.sh"