Macaulay2 1.26.05

.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 +77,4 @@ thets
 toom
 tring
 ue
+vew

.github/workflows/build-deb.yml

@@ -0,0 +1,101 @@
+# 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: uscan --verbose --rename --force-download
+      - name: Build package
+        run: |
+          cd macaulay2
+          git submodule update --init M2/Macaulay2/editors/emacs
+          if test ${{ matrix.os }} = "ubuntu-latest"; \
+          then dpkg-buildpackage; \
+          else dpkg-buildpackage -B; \
+          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-rpm.yml

@@ -42,7 +42,7 @@ 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/make-dist.yml

@@ -23,7 +23,7 @@ jobs:
           make doc-dist
       - name: Upload artifacts
         if: always()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: dist-tarballs
           path: |

.github/workflows/package-review.yml

@@ -25,7 +25,7 @@ jobs:
           package: ${{ github.event.inputs.package }}
 
       - name: Upload errors
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         if: failure()
         with:
            name: ${{ github.event.inputs.package }}-errors

.github/workflows/test_build.yml

@@ -39,17 +39,17 @@ jobs:
           - cmake
         os:
           - ubuntu-24.04
-          - macos-14
+          - macos-15
         compiler:
           - default
         include:
           # This build tests Clang rather than AppleClang (keep)
           - build-system: cmake
-            os: macos-14
+            os: macos-15
             compiler: brew-clang
         exclude:
           - build-system: cmake
-            os: macos-14
+            os: macos-15
             compiler: default
     steps:
       - uses: actions/checkout@v6
@@ -64,8 +64,7 @@ jobs:
           brew config
           brew update
           brew tap macaulay2/tap
-          brew install --overwrite python
-          brew install automake bison boost libtool tbb ccache ctags llvm make ninja yasm libffi msolve googletest fplll eigen
+          brew install automake bison boost libtool tbb ccache ctags llvm make yasm libffi msolve googletest fplll eigen jansson r
           brew install texinfo || true # sometimes post-install step fails
           brew install --only-dependencies macaulay2/tap/M2
           brew link factory --force
@@ -86,7 +85,7 @@ jobs:
                   libgivaro-dev libboost-regex-dev fflas-ffpack libflint-dev libmps-dev libfrobby-dev \
                   libsingular-dev singular-data libcdd-dev cohomcalg topcom 4ti2 libnormaliz-dev normaliz coinor-csdp \
                   libnauty-dev nauty lrslib polymake pipx phcpack w3c-markup-validator libtbb-dev qepcad libomp-16-dev \
-                  msolve libfplll-dev
+                  msolve libfplll-dev libjansson-dev r-base
 
 # ----------------------
 #   Steps common to all build variants
@@ -214,7 +213,7 @@ jobs:
       - name: Run Tests using Autotools
         if: matrix.build-system == 'autotools' && runner.os == 'Linux' && matrix.compiler == 'default'
         run: |
-          make check -o check-in-libraries
+          make -j$(nproc 2>/dev/null || sysctl -n hw.logicalcpu) check -o check-in-libraries
           make -C Macaulay2/html-check-links check
 
       - name: Validate HTML documentation
@@ -244,7 +243,7 @@ jobs:
 
       - name: Upload build logs
         if: always()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
            name: ${{ matrix.build-system }}-${{ matrix.os }}-${{ matrix.compiler }}-logs
            path: |
@@ -257,6 +256,7 @@ jobs:
              M2/BUILD/build/CMakeCache.txt
              M2/BUILD/build/CMakeFiles/CMakeError.log
              M2/BUILD/build/CMakeFiles/CMakeOutput.log
+             M2/BUILD/build/CMakeFiles/CMakeConfigureLog.yaml
              M2/BUILD/build/libraries/*/build/config.log
              # package example errors
              M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/*/example-output/*.errors
@@ -268,7 +268,7 @@ jobs:
 
       - name: Upload Macaulay2 package for Ubuntu (x86_64)
         if: matrix.build-system == 'cmake' && runner.os == 'Linux' && success()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: Macaulay2-${{ env.GIT_COMMIT }}-ubuntu-x86_64
           path: |

M2/BUILD/anton/Makefile

@@ -3,17 +3,19 @@ always:
 
 BRANCH := $(shell git branch --contains | grep '^\* ' | sed -e s=^..== -e s=/=.=g )
 
-cmake:
+cmake: # ~ mike's cmake-appleclang
 	echo "git branch is " $(BRANCH)
 	mkdir -p builds.tmp/$@
 	cd builds.tmp/$@; cmake \
 		-GNinja \
 		-DCMAKE_BUILD_TYPE=RelWithDebInfo \
-		-DCMAKE_PREFIX_PATH="`brew --prefix libomp`" \
+		-DCMAKE_PREFIX_PATH="`brew --prefix`;`brew --prefix factory`" \
+		-DBUILD_NATIVE=off \
+		-DCMAKE_INSTALL_PREFIX=`pwd`/installed \
 		-DBUILD_TESTING=on \
 		-DBUILD_DOCS=on \
+		-DCMAKE_EXPORT_COMPILE_COMMANDS=true \
 		../../../..
-#		-DLINTING=on
 
 auto:
 	echo "git branch is " $(BRANCH)

M2/BUILD/docker/fedora/Dockerfile

@@ -14,7 +14,7 @@ RUN microdnf install -y autoconf bison ccache chrpath cmake curl diffutils \
 
 # Libraries we require
 RUN microdnf install -y openblas-devel libxml2-devel readline-devel gdbm-devel \
-    boost-devel libomp-devel tbb-devel python3-devel libffi-devel
+    boost-devel libomp-devel tbb-devel python3-devel libffi-devel jansson-devel
 
 # Libraries we can build (factory not available on ubuntu)
 RUN microdnf install -y eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel \

M2/BUILD/docker/nightly/Dockerfile

@@ -2,32 +2,31 @@
 # Net usage:  ~100MB
 # Disk usage: <600MB docker image
 
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 RUN apt-get update && \
     apt-get install -y software-properties-common apt-transport-https curl git sudo unzip gnupg && \
     add-apt-repository -y ppa:macaulay2/macaulay2 && apt-get update && apt-get clean
 
 # this seems to be necessary because libstdc++6 is too old on Ubuntu 20.04
-RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test && apt-get update && \
-    apt-get install -y -q --no-install-recommends libomp5-11 && apt-get clean
+RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test && apt-get update && apt-get clean
 
 # Install Macaulay2
 COPY Macaulay2-*.zip /
 RUN unzip Macaulay2-*.zip && apt-get install -y /Macaulay2-*.deb
 
 # Install optional packages
-RUN apt-get install -y -q --no-install-recommends mlocate bash-completion && apt-get clean && updatedb
+RUN apt-get install -y -q --no-install-recommends locate bash-completion && apt-get clean && updatedb
 
 #RUN apt-get install -y -q --no-install-recommends emacs && apt-get clean
 
 # Add non-root user for building and running Macaulay2
-RUN useradd -G sudo -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+RUN useradd -G sudo -g root -o -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 USER 1000:0
 
 # Setting environment variables
-ENV LD_LIBRARY_PATH /usr/local/lib/Macaulay2/lib
-ENV PATH /usr/local/libexec/Macaulay2/bin:${PATH}
+ENV LD_LIBRARY_PATH=/usr/local/lib/Macaulay2/lib
+ENV PATH=/usr/local/libexec/Macaulay2/bin:${PATH}
 
 WORKDIR /home/macaulay
-ENTRYPOINT M2
+ENTRYPOINT ["M2"]

M2/BUILD/docker/rhel/Dockerfile

@@ -4,11 +4,13 @@ ARG RELEASE=latest
 FROM $DISTRIBUTION:$RELEASE
 
 # Install dependencies
+RUN dnf -y install 'dnf-command(config-manager)' || true
+RUN dnf config-manager --set-enabled crb || true # for jansson-devel
 RUN dnf -y install autoconf automake bison boost-devel bzip2 chrpath \
     cmake diffutils flex gcc-c++ gcc-gfortran git gmp-devel info     \
-    libffi-devel libtool libxml2-devel make mpfr-devel ncurses-devel \
-    patch python3-devel readline-devel rpm-build tbb-devel which     \
-    xz-devel zlib-devel
+    jansson-devel libffi-devel libtool libxml2-devel make mpfr-devel \
+    ncurses-devel patch python3-devel readline-devel rpm-build       \
+    tbb-devel which xz-devel zlib-devel
 RUN test "$RELEASE" != "8" && dnf -y install flexiblas-devel || true
 
 # Add non-root user for building and running Macaulay2

M2/BUILD/docker/testbot/Dockerfile

@@ -1,16 +1,16 @@
 # Time usage: <5min
 # Net usage:  <200MB
-# Disk usage: <800MB
+# Disk usage: <850MB
 
-FROM debian:bookworm
+FROM debian:trixie
 
 LABEL org.opencontainers.image.source=https://github.com/Macaulay2/M2
 
 # Setup the system
-RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates debian-keyring git && apt-get clean
+RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates wget git && apt-get clean
 
 # Install Macaulay2
-RUN echo "deb [signed-by=/usr/share/keyrings/debian-keyring.gpg] https://people.debian.org/~dtorrance/debian bookworm/" >> /etc/apt/sources.list && apt-get update && apt-get install -y --no-install-recommends macaulay2 4ti2 cohomcalg coinor-csdp gfan nauty normaliz topcom msolve && apt-get clean
+RUN wget -O /etc/apt/sources.list.d/macaulay2.sources https://macaulay2.com/Repositories/Debian/trixie/macaulay2.sources && apt-get update && apt-get install -y --no-install-recommends macaulay2 4ti2 cohomcalg coinor-csdp gfan nauty normaliz topcom msolve && apt-get clean
 
 # Add non-root user for using Macaulay2
 RUN useradd -G sudo -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers