Merge branch 'development' into stable1

Author: btotaro

.codespell_ignore

@@ -1,3 +1,4 @@
+aci
 afile
 alledges
 allready
@@ -45,11 +46,13 @@ lsat
 manuel
 methd
 mis
+mone
 mor
 multidimension
 nam
 nd
 nin
+ninj
 nome
 numer
 oint
@@ -74,3 +77,5 @@ thets
 toom
 tring
 ue
+vew
+matc

.github/workflows/build-deb.yml

@@ -0,0 +1,107 @@
+# This workflow builds Debian packages for the last 3 Debian releases
+# (currently trixie, bookworm, and bullseye)
+
+# After each Macaulay2 release, a new package is prepared for Debian unstable
+# (and a few days later, it migrates to Debian testing).  The packaging is
+# under version control in Debian's git forge, Salsa, at
+# https://salsa.debian.org/math-team/macaulay2, in the debian/latest branch
+
+# Backport the package to each of the supported releases and push to the
+# appropriate release branch, e.g., debian/trixie for trixie.  In many cases,
+# this is as simple as just merging the debian/latest branch.  Push each branch
+# to Salsa.
+
+# Once each branch is ready and pushed to Salsa, run this action using "workflow
+# dispatch" to generate each Debian package.
+
+# Download the artifacts and unzip them.  Push files using dput to
+# Repositories/Debian/mini-dinstall/incoming on the webserver, and then
+# run "mini-install -b -v" on the server.  Finally sign the Release files
+# in each directory (gpg --clearsign -o InRelease Release).
+
+name: Build Debian packages
+on: workflow_dispatch
+
+jobs:
+  build-deb:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        release:
+          - bullseye
+          - bookworm
+          - trixie
+        os:
+          - ubuntu-latest
+          - ubuntu-24.04-arm
+    container:
+      image: debian:${{ matrix.release }}
+    steps:
+      - name: Install dependencies
+        run: |
+          apt-get update
+          apt-get install -y wget ca-certificates
+          if test ${{ matrix.release }} = "bullseye"; \
+          then wget -O /usr/share/keyrings/macaulay2-archive-key.asc https://macaulay2.com/Repositories/Debian/macaulay2-archive-key.asc; \
+          fi
+          wget -O /etc/apt/sources.list.d/macaulay2.sources https://macaulay2.com/Repositories/Debian/${{ matrix.release }}/macaulay2.sources
+          apt-get update
+          apt-get install -y 4ti2 bison cohomcalg coinor-csdp \
+            debhelper dh-linktree emacs-nox fflas-ffpack flex \
+            gfan gfortran install-info libboost-dev libboost-math-dev \
+            libboost-regex-dev libboost-stacktrace-dev libcdd-dev \
+            libeigen3-dev libffi-dev libflint-dev libfrobby-dev libfplll-dev \
+            libgc-dev libgdbm-dev libglpk-dev libgtest-dev libjansson-dev \
+            liblapack-dev liblzma-dev libmathic-dev libmathicgb-dev \
+            libmemtailor-dev libmpfi-dev libmpfr-dev libmps-dev libnauty-dev \
+            libnormaliz-dev libntl-dev libreadline-dev \
+            libsingular4-dev libtbb-dev libxml2-dev lrslib \
+            lsb-release msolve nauty normaliz pkgconf python3-dev \
+            r-base singular-data time topcom git devscripts dh-elpa
+
+          # arch-independent dependencies (amd64 build only)
+          if test ${{ matrix.os }} = "ubuntu-latest"; then
+            apt-get install -y faketime gdbmtool jdupes
+
+            # don't need javascript on bullseye (just use the vendored copies)
+            if test ${{ matrix.release }} != "bullseye"; then
+              apt-get install -y node-fortawesome-fontawesome-free       \
+                fonts-katex libjs-bootsidemenu libjs-bootstrap5 libjs-d3 \
+                libjs-jquery libjs-katex libjs-nouislider libjs-three    \
+                node-clipboard node-css-loader node-import-local         \
+                node-interpret node-prismjs node-prismjs-bibtex          \
+                node-rechoir node-style-loader npm pkg-js-tools webpack
+            fi
+          fi
+      - name: Clone repository
+        run: |
+          git clone https://salsa.debian.org/math-team/macaulay2
+          cd macaulay2
+          git checkout debian/${{ matrix.release }}
+      - name: Generate tarball
+        run: |
+          cd macaulay2
+          uscan --verbose --rename --force-download
+      - name: Build source package
+        run: |
+          cd macaulay2
+          dpkg-buildpackage --build=source
+      - name: Build binary package
+        run: |
+          dpkg-source -x macaulay2_*.dsc
+          cd macaulay2-*
+          if test ${{ matrix.os }} = "ubuntu-latest"; \
+          then dpkg-buildpackage --build=binary;      \
+          else dpkg-buildpackage --build=any;         \
+          fi
+      - name: Upload build logs
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: ${{ matrix.os }}-debian-${{ matrix.release }}
+          path: |
+            *.build
+            *.buildinfo
+            *.changes
+            *.deb

.github/workflows/build-dmg.yml

@@ -0,0 +1,156 @@
+# This workflow builds a macOS DMG for distributing Macaulay2.
+# It runs on both Intel (x86_64) and Apple Silicon (arm64) runners.
+#
+# The resulting DMG presents a Macaulay2-VERSION directory alongside a
+# shortcut to /Applications so users can drag it there.  After installation,
+# users add /Applications/Macaulay2-VERSION/bin to their PATH.
+
+name: Build macOS DMG
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'release-*'
+
+defaults:
+  run:
+    working-directory: M2/BUILD/dmg
+
+jobs:
+  build-dmg:
+    name: Build DMG (${{ matrix.arch }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: macos-14
+            arch: arm64
+            deployment_target: "14.0"
+          - os: macos-15-intel
+            arch: x86_64
+            deployment_target: "15.0"
+
+    steps:
+      - uses: actions/checkout@v6
+
+# ----------------------
+#   Install Homebrew dependencies
+# ----------------------
+
+      - name: Install requirements
+        run: |
+          brew config
+          brew update
+          brew tap macaulay2/tap
+          # Build tools
+          brew install automake bison dylibbundler ccache ctags llvm make yasm googletest r
+          brew install texinfo || true
+          # M2 library dependencies
+          brew install \
+              bdw-gc boost eigen fplll jansson libffi tbb \
+              macaulay2/tap/factory fflas-ffpack flint frobby givaro \
+              mpfi mpsolve ntl \
+              memtailor mathic mathicgb
+          brew link macaulay2/tap/factory --force
+          # External programs bundled into the DMG
+          brew install 4ti2 cohomcalg csdp gfan lrs msolve nauty normaliz topcom
+
+# ----------------------
+#   Set up build environment
+# ----------------------
+
+      - name: Prepare build environment
+        run: |
+          echo "$(brew --prefix ccache)/libexec"         >> $GITHUB_PATH
+          echo "$(brew --prefix make)/libexec/gnubin"    >> $GITHUB_PATH
+          echo "$(brew --prefix libtool)/libexec/gnubin" >> $GITHUB_PATH
+          echo "$(brew --prefix bison)/bin"              >> $GITHUB_PATH
+          echo "CPPFLAGS=-I$(brew --prefix)/include -I$(brew --prefix libomp)/include -I$(brew --prefix readline)/include" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$(brew --prefix)/lib -L$(brew --prefix libomp)/lib -L$(brew --prefix readline)/lib"             >> $GITHUB_ENV
+          M2_VERSION=$(cat ../../VERSION)
+          echo "M2_VERSION=$M2_VERSION"         >> $GITHUB_ENV
+          echo "PKG_NAME=Macaulay2-$M2_VERSION" >> $GITHUB_ENV
+
+# ----------------------
+#   Download external programs not available on Homebrew
+# ----------------------
+
+      - name: Download external programs
+        run: |
+          # phcpack (universal binary)
+          curl -fsSL https://github.com/janverschelde/PHCpack/releases/download/v2.4.92/macphc \
+            -o "$RUNNER_TEMP/phc"
+          chmod +x "$RUNNER_TEMP/phc"
+
+          # bertini (arm64 only)
+          if [ "${{ matrix.arch }}" = "arm64" ]; then
+            curl -fsSL https://bertini.nd.edu/BertiniApple_v1.7.tar.gz \
+              | tar -xz -C "$RUNNER_TEMP"
+            cp "$RUNNER_TEMP/BertiniApple_v1.7/bertini" "$RUNNER_TEMP/bertini"
+            chmod +x "$RUNNER_TEMP/bertini"
+          fi
+
+# ----------------------
+#   Build Macaulay2 and create DMG
+# ----------------------
+
+      - name: Build and package Macaulay2
+        env:
+          WORKSPACE: ${{ github.workspace }}
+          ARCH: ${{ matrix.arch }}
+          DEPLOYMENT_TARGET: ${{ matrix.deployment_target }}
+        run: make all
+
+# ----------------------
+#   Test the DMG
+# ----------------------
+
+      - name: Install DMG
+        env:
+          WORKSPACE: ${{ github.workspace }}
+          ARCH: ${{ matrix.arch }}
+        run: make install-dmg
+
+      - name: Run basic tests
+        env:
+          WORKSPACE: ${{ github.workspace }}
+          ARCH: ${{ matrix.arch }}
+        run: make run-basic-tests
+
+      - name: Run core tests
+        env:
+          WORKSPACE: ${{ github.workspace }}
+          ARCH: ${{ matrix.arch }}
+        run: make run-core-tests
+
+      - name: Run package tests
+        # x86_64 runners are too slow and time out on --check 3
+        if: matrix.arch == 'arm64'
+        env:
+          WORKSPACE: ${{ github.workspace }}
+          ARCH: ${{ matrix.arch }}
+        run: make run-package-tests
+
+# ----------------------
+#   Upload artifacts
+# ----------------------
+
+      - name: Upload build logs
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: ${{ env.PKG_NAME }}-${{ matrix.arch }}-logs
+          path: |
+            M2/BUILD/build/config.log
+            M2/BUILD/build/include/*
+            M2/BUILD/build/libraries/*/build/*/config.log
+
+      - name: Upload DMG
+        if: success()
+        uses: actions/upload-artifact@v7
+        with:
+          name: ${{ env.PKG_NAME }}-${{ matrix.arch }}-macOS
+          path: "*.dmg"
+          retention-days: 7

.github/workflows/build-rpm.yml

@@ -1,5 +1,9 @@
 name: Build RPM packages
-on: workflow_dispatch
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'release-*'
 
 jobs:
   build-rpm:
@@ -17,16 +21,16 @@ jobs:
           - 8
           - 9
           - 10
-          - 41
           - 42
           - 43
+          - 44
         exclude:
-          - distribution: almalinux
-            release: 41
           - distribution: almalinux
             release: 42
           - distribution: almalinux
             release: 43
+          - distribution: almalinux
+            release: 44
           - distribution: fedora
             release: 8
           - distribution: fedora
@@ -42,7 +46,7 @@ jobs:
           RELEASE=${{ matrix.release }}
       - name: Upload artifacts
         if: always()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.os }}-${{ matrix.distribution }}-${{ matrix.release }}
           path: |

.github/workflows/docker-testbot.yml

@@ -0,0 +1,43 @@
+# This workflow builds the Macaulay2 testbot Docker image from
+# M2/BUILD/docker/testbot/Dockerfile and pushes it to GitHub Packages,
+# tagged with the current Macaulay2 version (see M2/VERSION) and "latest".
+#
+# The resulting image is published at
+# https://github.com/Macaulay2/M2/pkgs/container/testbot
+
+name: Build and push testbot Docker image
+
+on: workflow_dispatch
+
+env:
+  IMAGE_NAME: ghcr.io/macaulay2/testbot
+
+jobs:
+  docker-testbot:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Determine image tags
+        run: |
+          M2_VERSION=$(cat M2/VERSION)
+          echo "M2_VERSION=$M2_VERSION" >> "$GITHUB_ENV"
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push image
+        uses: docker/build-push-action@v6
+        with:
+          context: M2/BUILD/docker/testbot
+          push: true
+          tags: |
+            ${{ env.IMAGE_NAME }}:v${{ env.M2_VERSION }}
+            ${{ env.IMAGE_NAME }}:latest