Merge branch 'develop' into circuits_matroid

.ci/merge-fixes.sh

@@ -1,5 +1,8 @@
 #!/bin/sh
-# Apply open PRs labeled "blocker" from sagemath/sage as patches.
+# Apply open PRs labeled "p: CI Fix" from sagemath/sage as patches.
+# (policy set by vote in 2024-03,
+#  https://groups.google.com/g/sage-devel/c/OKwwUGyKveo/m/vpyCXYBqAAAJ)
+#
 # This script is invoked by various workflows in .github/workflows
 #
 # The repository variable SAGE_CI_FIXES_FROM_REPOS can be set
@@ -20,15 +23,15 @@ for REPO in ${SAGE_CI_FIXES_FROM_REPOSITORIES:-sagemath/sage}; do
             echo "Nothing to do for 'none' in SAGE_CI_FIXES_FROM_REPOSITORIES"
             ;;
         */*)
-            echo "Getting open PRs with 'blocker' status from https://github.com/$REPO/pulls?q=is%3Aopen+label%3A%22p%3A+blocker+%2F+1%22"
+            echo "Getting open PRs with 'p: CI Fix' label from https://github.com/$REPO/pulls?q=is%3Aopen+label%3A%22p%3A+CI+Fix%22"
             GH="gh -R $REPO"
             REPO_FILE="upstream/ci-fixes-${REPO%%/*}-${REPO##*/}"
-            PRs="$($GH pr list --label "p: blocker / 1" --json number --jq '.[].number' | tee $REPO_FILE)"
+            PRs="$($GH pr list --label "p: CI Fix" --json number --jq '.[].number' | tee $REPO_FILE)"
             date -u +"%Y-%m-%dT%H:%M:%SZ" > $REPO_FILE.date  # Record the date, for future reference
             if [ -z "$PRs" ]; then
-                echo "Nothing to do: Found no open PRs with 'blocker' status in $REPO."
+                echo "Nothing to do: Found no open PRs with 'p: CI Fix' label in $REPO."
             else
-                echo "Found open PRs with 'blocker' status in $REPO: $(echo $PRs)"
+                echo "Found open PRs with 'p: CI Fix' label in $REPO: $(echo $PRs)"
                 git tag -f test_base
                 git commit -q -m "Uncommitted changes" --no-allow-empty -a
                 for a in $PRs; do

.github/workflows/build.yml

@@ -373,6 +373,6 @@ jobs:
 
       - name: Upload coverage to codecov
         if: (success() || failure()) && steps.container.outcome == 'success'
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           directory: ./coverage-report

.github/workflows/ci-conda.yml

@@ -61,7 +61,7 @@ jobs:
             ${{ runner.os }}-conda-${{ hashFiles('src/environment-3.11.yml') }}
 
       - name: Setup Conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python }}
           miniforge-version: latest

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

@@ -47,7 +47,7 @@ jobs:
       - uses: actions/checkout@v4
       - name: Get all packages that have changed
         id: changed-packages
-        uses: tj-actions/changed-files@v42
+        uses: tj-actions/changed-files@v44
         with:
           files_yaml: |
             configures:

.github/workflows/dist.yml

@@ -37,16 +37,37 @@ jobs:
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install $(build/bin/sage-get-system-packages debian _bootstrap)
       - name: make dist (--disable-download-from-upstream-url)
+        id: make_dist
         run: |
           ./bootstrap -D && ./configure --disable-download-from-upstream-url && make dist
         env:
           MAKE: make -j8
+      - name: make download (--disable-download-from-upstream-url)
+        id: make_download
+        run: |
+          make -k download DOWNLOAD_PACKAGES=":all: --no-file huge"
+        env:
+          MAKE: make -j8
+      - name: Reconfigure with --enable-download-from-upstream-url
+        if: (success() || failure()) && (steps.make_dist.outcome != 'success' || steps.make_download.outcome != 'success')
+        run: |
+          ./configure
       - name: make dist (--enable-download-from-upstream-url)
-        if: failure()
+        if: (success() || failure()) && steps.make_dist.outcome != 'success'
         run: |
-          ./configure && make dist
+          make dist
         env:
           MAKE: make -j8
+      - name: make download (--enable-download-from-upstream-url)
+        if: (success() || failure()) && steps.make_download.outcome != 'success'
+        run: |
+          make -k download DOWNLOAD_PACKAGES=":all: --no-file huge --allow-upstream"
+        env:
+          MAKE: make -j8
+      - name: Remove what cannot be distributed
+        if: success() || failure()
+        run: |
+          rm -f upstream/*do-not-distribute*
       - uses: actions/upload-artifact@v4
         if: success() || failure()
         with:
@@ -64,7 +85,7 @@ jobs:
       - uses: actions/download-artifact@v4
         with:
           name: release_dist
-      - uses: softprops/action-gh-release@v1
+      - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
           files: |

.github/workflows/doc-build-pdf.yml

@@ -40,7 +40,7 @@ jobs:
           - 5000:5000
     steps:
       - name: Maximize build disk space
-        uses: easimon/maximize-build-space@v8
+        uses: easimon/maximize-build-space@v10
         with:
           # need space in /var for Docker images
           root-reserve-mb:      30000

.github/workflows/doc-build.yml

@@ -44,7 +44,7 @@ jobs:
           - 5000:5000
     steps:
       - name: Maximize build disk space
-        uses: easimon/maximize-build-space@v8
+        uses: easimon/maximize-build-space@v10
         with:
           # need space in /var for Docker images
           root-reserve-mb:      30000

.github/workflows/lint.yml

@@ -1,11 +1,11 @@
 name: Lint
 
-on: 
+on:
   push:
     branches:
       - master
       - develop
-  pull_request: 
+  pull_request:
   merge_group:
 
 concurrency:
@@ -29,7 +29,7 @@ jobs:
         SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 

.gitignore

@@ -235,16 +235,16 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-categories/pyproject.toml
 /pkgs/sagemath-environment/pyproject.toml
 /pkgs/sagemath-repl/pyproject.toml
-/pkgs/sagemath-objects/requirements.txt
-/pkgs/sagemath-bliss/requirements.txt
-/pkgs/sagemath-coxeter3/requirements.txt
-/pkgs/sagemath-mcqd/requirements.txt
-/pkgs/sagemath-meataxe/requirements.txt
-/pkgs/sagemath-sirocco/requirements.txt
-/pkgs/sagemath-tdlib/requirements.txt
-/pkgs/sagemath-categories/requirements.txt
-/pkgs/sagemath-environment/requirements.txt
-/pkgs/sagemath-repl/requirements.txt
+/pkgs/sagemath-objects/requirements*.txt
+/pkgs/sagemath-bliss/requirements*.txt
+/pkgs/sagemath-coxeter3/requirements*.txt
+/pkgs/sagemath-mcqd/requirements*.txt
+/pkgs/sagemath-meataxe/requirements*.txt
+/pkgs/sagemath-sirocco/requirements*.txt
+/pkgs/sagemath-tdlib/requirements*.txt
+/pkgs/sagemath-categories/requirements*.txt
+/pkgs/sagemath-environment/requirements*.txt
+/pkgs/sagemath-repl/requirements*.txt
 /pkgs/sagemath-categories/MANIFEST.in
 
 # same for old locations - before Issue #31577

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.4.beta5
-doi: 10.5281/zenodo.593563
-date-released: 2024-05-02
+version: 10.4.beta6
+doi: 10.5281/zenodo.8042260
+date-released: 2024-05-12
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

CITATION.cff.in

@@ -5,7 +5,7 @@ abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
 version: ${SAGE_VERSION}
-doi: 10.5281/zenodo.593563
+doi: 10.5281/zenodo.8042260
 date-released: ${SAGE_RELEASE_DATE}
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

Makefile

@@ -79,10 +79,11 @@ reconfigure:
 	fi
 
 # Preemptively download all source tarballs of normal packages.
+DOWNLOAD_PACKAGES=:all:
 download:
 	export SAGE_ROOT=$$(pwd) && \
 	export PATH=$$SAGE_ROOT/build/bin:$$PATH && \
-	sage-package download :all:
+	sage-package download $(DOWNLOAD_PACKAGES)
 
 dist: build/make/Makefile
 	./sage --sdist

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.4.beta5, Release Date: 2024-05-02
+SageMath version 10.4.beta6, Release Date: 2024-05-12

build/bin/sage-get-system-packages

@@ -50,6 +50,12 @@ case "$SYSTEM" in
         ;;
 esac
 
+case "$SPKGS" in
+    *pkg:*|pypi/*|generic/*)
+        PATH="${SAGE_ROOT}/build/bin:$PATH" SPKGS=$(sage-package list $SPKGS)
+        ;;
+esac
+
 for PKG_BASE in $SPKGS; do
     if [ $FROM_PYPROJECT_TOML -eq 1 ]; then
         if [ -f "$SAGE_ROOT/src/pyproject.toml" ]; then

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=599182ff950764df31446f7bf8350499717dc76e
-md5=06e0643f4948ad4b4c87d2530d026a1f
-cksum=4286155814
+sha1=dca19f73642b76f1f96b860bb6603499f586380d
+md5=cdfc81ecaa40045a7827959e9f52e226
+cksum=1337053183

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-e77b3df44ade2f51f750de90ad255f772a933776
+f5e78840b108412e1e26382910af993f874c6933

build/pkgs/cython/checksums.ini

@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=48f0535ce0b05e0e4ae4daa6a597a2cdd76274f5
-md5=94ab8466d9350a31cfef3a0853c2fea5
-cksum=2507297160
+sha1=83d6428e3bb7869f44f92ed75d7dff867c2a38ce
+md5=0110d7adac5ebb6ae65d8b71a72b664e
+cksum=1043698601
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-3.0.7
+3.0.10

build/pkgs/fflas_ffpack/checksums.ini

@@ -1,4 +1,5 @@
 tarball=fflas_ffpack-VERSION.tar.bz2
-sha1=c221513710b98e0e62153f424a9725c5be2ff62a
-md5=05c77ea30394cacd53b7aed6ffba1e7b
-cksum=3775757878
+sha1=7c5faa81abc2b88ec24cec373b5e44cbaa7844dd
+md5=d8b7c113951a2a3f498a3aaadbe5620f
+cksum=3321469120
+upstream_url=https://github.com/linbox-team/fflas-ffpack/releases/download/vVERSION/fflas_ffpack-VERSION.tar.bz2

build/pkgs/fflas_ffpack/package-version.txt

@@ -1 +1 @@
-2.4.3.p0
+2.5.0

build/pkgs/fflas_ffpack/patches/357.patch

@@ -0,0 +1,35 @@
+From 9b6083c663096e9ca85775b79f1f27c848dbeb98 Mon Sep 17 00:00:00 2001
+From: Cyril Bouvier <cyril.bouvier@lirmm.fr>
+Date: Fri, 17 Dec 2021 10:27:02 +0100
+Subject: [PATCH] Fix SimdChooser: on not x86_64 machines its value could be an
+ nonexistant struct
+
+---
+ fflas-ffpack/fflas/fflas_simd.h | 14 ++++++++++++++
+ 1 file changed, 14 insertions(+)
+
+diff --git a/fflas-ffpack/fflas/fflas_simd.h b/fflas-ffpack/fflas/fflas_simd.h
+index bf5d30211..84ced0fd8 100644
+--- a/fflas-ffpack/fflas/fflas_simd.h
++++ b/fflas-ffpack/fflas/fflas_simd.h
+@@ -384,6 +384,20 @@ struct SimdChooser<T, true, true> // integral number
+ #endif
+ };
+
++#ifndef __x86_64__
++template <>
++struct SimdChooser<uint64_t, true, true>
++{
++    using value = NoSimd<uint64_t>;
++};
++
++template <>
++struct SimdChooser<int64_t, true, true>
++{
++    using value = NoSimd<int64_t>;
++};
++#endif
++
+ template <class T> using Simd = typename SimdChooser<T>::value;
+
+ // template <class T> struct SimdChooser<T, true> {