Merge branch 'development' into locate

Macaulay2 · Aug 8, 2024 · a867e8d · a867e8d
2 parents 0644561 + bf9ac3e
commit a867e8d
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diff --git a/.github/workflows/test_build.yml b/.github/workflows/test_build.yml
@@ -10,17 +10,17 @@ name: Build and Test Macaulay2
 
 on:
   workflow_dispatch:
-  push:
-    branches:
-      - pre-master # when we're ready to merge 'development' into 'master', we merge it first into 'pre-master', so it can be tested
   pull_request:
     branches:
       - master
       - development
   schedule:
-    # cron time in UTC
-    # a scheduled job runs on the default branch: 'master'
-    - cron: '0 6 * * *'
+    - cron: '0 6 * * SUN' # runs tests on the main branch every Sunday at 06:00 UTC
+
+concurrency:
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 defaults:
   run:
@@ -35,28 +35,23 @@ jobs:
       fail-fast: false
       matrix:
         build-system:
-          - cmake
           - autotools
+          - cmake
         os:
-          - ubuntu-22.04
-          - macos-12
+          - ubuntu-24.04
+          - macos-13
         compiler:
           - default
         include:
-          - build-system: cmake
-            os: ubuntu-22.04
-            compiler: clang-15
-            cxx: clang++-15
-            cc: clang-15
           # This build tests Clang rather than AppleClang (keep)
           - build-system: cmake
-            os: macos-12
+            os: macos-13 # TODO: switch to macos-14 for arm64 testing
             compiler: clang-15
             cxx: clang++
             cc: clang
         exclude:
           - build-system: cmake
-            os: macos-12
+            os: macos-13
             compiler: default
     steps:
       - uses: actions/checkout@v4
@@ -70,8 +65,10 @@ jobs:
         run: |
           brew config
           brew tap macaulay2/tap
-          brew install automake boost tbb ccache ctags llvm make ninja yasm libffi
+          brew install --overwrite python
+          brew install automake boost tbb ccache ctags texinfo llvm make ninja yasm libffi msolve
           brew install --only-dependencies macaulay2/tap/M2
+          brew link factory --force
 
 # ----------------------
 #   Install missing tools and libraries for Linux
@@ -80,14 +77,15 @@ jobs:
       - name: Install requirements for Linux
         if: runner.os == 'Linux'
         run: |
+          sudo add-apt-repository -y -n ppa:macaulay2/macaulay2
           sudo apt-get update
-          sudo apt-get install -y -q --no-install-recommends clang-15 gfortran libtool-bin ninja-build yasm ccache
-          sudo apt-get install -y -q --no-install-recommends libboost-stacktrace-dev \
+          sudo apt-get install -y -q --no-install-recommends clang-16 gfortran libtool-bin ninja-build yasm ccache
+          sudo apt-get install -y -q --no-install-recommends liblzma-dev libboost-stacktrace-dev \
                   libncurses-dev libncurses5-dev libreadline-dev libeigen3-dev liblapack-dev libxml2-dev \
                   libgc-dev libgdbm-dev libglpk-dev libgmp3-dev libgtest-dev libmpfr-dev libmpfi-dev libntl-dev gfan \
                   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 \
-                  libnauty2-dev nauty lrslib polymake phcpack w3c-markup-validator libtbb-dev qepcad libomp-15-dev
+                  libnauty-dev nauty lrslib polymake pipx phcpack w3c-markup-validator libtbb-dev qepcad libomp-16-dev msolve
 
 # ----------------------
 #   Steps common to all build variants
@@ -99,7 +97,7 @@ jobs:
           echo "CXX=${{ matrix.cxx }}" >> $GITHUB_ENV
           if [[ "${{ runner.os }}" == "Linux" ]]
           then shopt -s expand_aliases
-               alias llvm-config="/usr/bin/llvm-config-15"
+               alias llvm-config="/usr/bin/llvm-config-16"
                echo "/usr/lib/ccache"                     >> $GITHUB_PATH
                echo "/home/linuxbrew/.linuxbrew/bin"      >> $GITHUB_PATH
           else echo `brew --prefix ccache`/libexec        >> $GITHUB_PATH
@@ -144,7 +142,7 @@ jobs:
         if: matrix.build-system == 'cmake'
         run: |
           cmake --build . --target M2-core M2-emacs install-packages
-          if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.compiler }}" == "clang-15" ]]; then
+          if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.build-system }}" == "cmake" ]]; then
               sudo apt-get install -y -q --no-install-recommends dpkg-dev
               echo "GIT_COMMIT=`git describe --dirty --always --match HEAD`" >> $GITHUB_ENV
               cpack -G DEB
@@ -175,7 +173,7 @@ jobs:
 # ----------------------
 
       - name: Run Tests using CTest
-        if: matrix.build-system == 'cmake' && runner.os == 'Linux' && matrix.compiler == 'clang-15'
+        if: matrix.build-system == 'cmake' && runner.os == 'macOS'
         run: |
           set -xe
           ./M2 -q --check 1 -e 'exit 0'
@@ -197,7 +195,7 @@ jobs:
       - name: Validate HTML documentation
         if: matrix.build-system == 'autotools' && runner.os == 'Linux'
         run: |
-          python3 -m pip install html5validator
+          pipx install html5validator
           if test ${{ github.event_name }} = pull_request
           then
             git fetch --depth=1 origin development
@@ -243,7 +241,7 @@ jobs:
              M2/BUILD/build/Macaulay2/tests/*/*.errors
 
       - name: Upload Macaulay2 package for Ubuntu (x86_64)
-        if: matrix.build-system == 'cmake' && runner.os == 'Linux' && matrix.compiler == 'clang-15' && success()
+        if: matrix.build-system == 'cmake' && runner.os == 'Linux' && success()
         uses: actions/upload-artifact@v4
         with:
           name: Macaulay2-${{ env.GIT_COMMIT }}-ubuntu-x86_64

diff --git a/M2/BUILD/docker/actions/Dockerfile b/M2/BUILD/docker/actions/Dockerfile
@@ -2,36 +2,39 @@
 # Net usage:  ~255MB
 # Disk usage: <1GB docker image + 650MB Macaulay2 build
 
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
 RUN apt-get update && \
     apt-get install -y software-properties-common apt-transport-https build-essential curl git gnupg && \
     curl https://apt.kitware.com/keys/kitware-archive-latest.asc -s --output - | apt-key add - && \
-    echo 'deb https://apt.kitware.com/ubuntu/ focal main' > \
+    echo 'deb https://apt.kitware.com/ubuntu/ noble main' > \
       /etc/apt/sources.list.d/cmake.list && \
     add-apt-repository -y ppa:macaulay2/macaulay2 && \
     apt-get update && apt-get install -y autoconf bison ccache cmake flex libtool ninja-build yasm && apt-get clean
 
 # Programs and libraries we require to build
-RUN apt-get install -y -q --no-install-recommends libatomic-ops-dev libboost-stacktrace-dev \
+RUN apt-get install -y -q --no-install-recommends libboost-stacktrace-dev \
 	libncurses-dev libncurses5-dev libreadline-dev libeigen3-dev liblapack-dev libxml2-dev \
-	libgc-dev libgdbm-dev libglpk-dev libgmp3-dev libgtest-dev libmpfr-dev libntl-dev gfan \
+	libgc-dev libgdbm-dev libglpk-dev libgmp3-dev libgtest-dev libmpfr-dev libmpfi-dev libntl-dev gfan \
 	libgivaro-dev libboost-regex-dev fflas-ffpack libflint-dev libmps-dev libfrobby-dev \
 	libnauty-dev libnormaliz-dev libsingular-dev singular-data libcdd-dev \
-	cohomcalg topcom 4ti2 normaliz coinor-csdp nauty lrslib w3c-markup-validator libtbb-dev
+	cohomcalg topcom 4ti2 normaliz coinor-csdp nauty lrslib libtbb-dev
 
 # Testing with clang-11 compiler
-RUN apt-get install -y clang-11 llvm-11 && apt-get clean
+#RUN apt-get install -y clang-16 llvm-16 libomp-16-dev && apt-get clean
 
-RUN apt-get install -y -q --no-install-recommends mlocate bash-completion && apt-get clean && updatedb
+# For testing optional programs
+#RUN apt-get install -y polymake phcpack qepcad && apt-get clean
+
+RUN apt-get install -y -q --no-install-recommends locate bash-completion && apt-get clean && updatedb
 
 RUN add-apt-repository ppa:ubuntu-toolchain-r/test && \
     apt-get update
 
 # Needed for building with autotools
-# RUN apt-get install -y -q liblzma-dev
+# RUN apt-get install -y -q liblzma-dev w3c-markup-validator
 
 # Add non-root user for building and running Macaulay2
 RUN useradd -G sudo -g root -u 1000 -m macaulay

diff --git a/M2/BUILD/docker/arch/Dockerfile b/M2/BUILD/docker/arch/Dockerfile
@@ -22,7 +22,7 @@ RUN pacman --sync --noconfirm --refresh --needed \
 RUN pacman --sync --noconfirm --needed openblas openmp intel-tbb libxml2 readline gdbm boost
 
 # Libraries we can build
-RUN pacman --sync --noconfirm --needed eigen fflas-ffpack givaro glpk gmp gc gtest mpfr ntl libatomic_ops
+RUN pacman --sync --noconfirm --needed eigen fflas-ffpack givaro glpk gmp gc gtest mpfr ntl
 
 # Optional packages
 RUN pacman --sync --noconfirm mlocate bash-completion

diff --git a/M2/BUILD/docker/brew/Dockerfile b/M2/BUILD/docker/brew/Dockerfile
@@ -2,7 +2,7 @@
 # Net usage:  ~700MB
 # Disk usage: ~1GB
 
-FROM homebrew/brew
+FROM homebrew/ubuntu22.04:latest
 
 # Install optional packages
 RUN apt-get update && apt-get install -y -q --no-install-recommends vim mlocate && apt-get clean

diff --git a/M2/BUILD/docker/debian/Dockerfile b/M2/BUILD/docker/debian/Dockerfile
@@ -16,9 +16,6 @@ RUN apt-get install -y libopenblas-dev libxml2-dev libreadline-dev libgdbm-dev \
 	libboost-regex-dev libboost-stacktrace-dev libomp-dev libtbb-dev && \
 	apt-get clean
 
-# This is a dependency that we should get rid of
-RUN apt-get install -y libatomic-ops-dev && apt-get clean
-
 # Libraries we can build (factory not available on ubuntu)
 RUN apt-get install -y libeigen3-dev  libglpk-dev libgmp3-dev libmpfr-dev \
       libntl-dev libnauty-dev libnormaliz-dev libfrobby-dev libgc-dev && apt-get clean

diff --git a/M2/BUILD/docker/fedora/Dockerfile b/M2/BUILD/docker/fedora/Dockerfile
@@ -11,7 +11,7 @@ RUN microdnf install autoconf bison ccache cmake curl diffutils file gcc-c++ git
 
 # Libraries we require
 RUN microdnf install openblas-devel libxml2-devel readline-devel gdbm-devel \
-	boost-devel libatomic_ops-devel libomp-dev libtbb-dev
+	boost-devel libomp-dev libtbb-dev
 
 # Libraries we can build (factory not available on ubuntu)
 RUN microdnf install eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel \

diff --git a/M2/BUILD/docker/gentoo/Dockerfile b/M2/BUILD/docker/gentoo/Dockerfile
@@ -15,7 +15,7 @@ COPY --from=portage /var/db/repos/gentoo /var/db/repos/gentoo
 RUN emerge --sync
 RUN emerge -n cmake ninja
 
-#RUN emerge --ask -n 4ti2 blas-reference lapack-reference boehm-gc boost cddlib coinor-csdp flint fplll frobby gdbm gfan glpk gmp gtest libatomic_ops lrslib mpc mpfr mpir nauty normaliz ntl topcom yasm sys-process/time
+#RUN emerge --ask -n 4ti2 blas-reference lapack-reference boehm-gc boost cddlib coinor-csdp flint fplll frobby gdbm gfan glpk gmp gtest lrslib mpc mpfr mpir nauty normaliz ntl topcom yasm sys-process/time
 
 #  	autoconf automake bison make patch ccache \
 #	gettext python cmake curl gcc git gnupg \
@@ -25,7 +25,7 @@ RUN emerge -n cmake ninja
 #RUN pacman --sync --noconfirm --needed openblas openmp intel-tbb libxml2 readline gdbm boost
 
 # Libraries we can build
-#RUN pacman --sync --noconfirm --needed eigen fflas-ffpack givaro glpk gmp gc gtest mpfr ntl libatomic_ops
+#RUN pacman --sync --noconfirm --needed eigen fflas-ffpack givaro glpk gmp gc gtest mpfr ntl
 
 # Optional packages
 #RUN pacman --sync --noconfirm mlocate bash-completion

diff --git a/M2/BUILD/docker/ubuntu/Dockerfile b/M2/BUILD/docker/ubuntu/Dockerfile
@@ -2,13 +2,13 @@
 # Net usage:  ~255MB
 # Disk usage: <1GB docker image + 650MB Macaulay2 build
 
-FROM ubuntu:focal
+FROM ubuntu:noble
 
 # Programs we require to build
 RUN apt-get update && \
     apt-get install -y apt-transport-https build-essential curl git gnupg && \
     curl https://apt.kitware.com/keys/kitware-archive-latest.asc -s --output - | apt-key add - && \
-    echo 'deb https://apt.kitware.com/ubuntu/ focal main' > \
+    echo 'deb https://apt.kitware.com/ubuntu/ noble main' > \
       /etc/apt/sources.list.d/cmake.list && \
     apt-get update && apt-get install -y autoconf bison ccache cmake flex libtool ninja-build yasm && apt-get clean
 
@@ -20,14 +20,11 @@ RUN apt-get install -y libopenblas-dev libxml2-dev libreadline-dev libgdbm-dev \
 	libboost-regex-dev libboost-stacktrace-dev libomp-dev libtbb-dev && \
 	apt-get clean
 
-# This is a dependency that we should get rid of
-RUN apt-get install -y libatomic-ops-dev && apt-get clean
-
 # Libraries we can build
 RUN apt-get install -y --no-install-recommends software-properties-common && \
     add-apt-repository -y ppa:macaulay2/macaulay2 && apt-get update && \
     apt-get install -y -q --no-install-recommends libeigen3-dev libgc-dev \
-	libglpk-dev libgmp3-dev libmpfr-dev libmps-dev libgtest-dev \
+	libglpk-dev libgmp3-dev libmpfr-dev libmpfi-dev libmps-dev libgtest-dev \
 	libntl-dev libflint-dev libsingular-dev singular-data libfrobby-dev \
 	libnauty-dev libnormaliz-dev && apt-get clean
 
@@ -43,7 +40,6 @@ RUN apt-get update && \
     apt-get update && apt-get clean
 
 RUN apt-get install -y libgivaro-dev fflas-ffpack
-RUN apt-get install -y libmpfi-dev
 
 # Optional packages
 RUN apt-get install -y mlocate bash-completion

diff --git a/M2/BUILD/docker/valgrind/Dockerfile b/M2/BUILD/docker/valgrind/Dockerfile
@@ -20,9 +20,6 @@ RUN apt-get install -y libopenblas-dev libxml2-dev libreadline-dev libgdbm-dev \
 	libboost-regex-dev libboost-stacktrace-dev libomp-dev libtbb-dev && \
 	apt-get clean
 
-# This is a dependency that we should get rid of
-RUN apt-get install -y libatomic-ops-dev && apt-get clean
-
 # Libraries we can build
 RUN apt-get install -y --no-install-recommends software-properties-common && \
     add-apt-repository -y ppa:macaulay2/macaulay2 && apt-get update && \

diff --git a/M2/CMakeLists.txt b/M2/CMakeLists.txt
@@ -14,9 +14,9 @@
 ##  6. cmake --install BUILD/cmake
 ###############################################################################
 
-## Requires CMake version 3.15 and is tested with 3.19
-cmake_minimum_required(VERSION 3.15...3.19)
-cmake_policy(VERSION 3.14)
+## Requires CMake version 3.24 and is tested with 3.30
+cmake_minimum_required(VERSION 3.24...3.30)
+cmake_policy(VERSION 3.24)
 cmake_policy(SET CMP0096 NEW) # preserve leading zeros in version number
 
 ## Use the C++20 standard

diff --git a/M2/LICENSING-NOTES b/M2/LICENSING-NOTES
@@ -49,6 +49,7 @@ Programs we include with our distribution:
 
 	    	4ti2			GPL 2
 	        gfan		        GPL 2
+		msolve			GPL 2
 	        normaliz		GPL 3
 
 Libraries linked with some of our programs:

diff --git a/M2/Macaulay2/README.in b/M2/Macaulay2/README.in
@@ -30,7 +30,7 @@ fitness for a particular purpose.
 
 Some programs or packages may be distributed along with Macaulay2 according to the terms of
 their own licenses, not affecting the license we offer you for Macaulay2
-itself.  These include the following programs: 4ti2, normaliz, and gfan.
+itself.  These include the following programs: 4ti2, normaliz, gfan, and msolve.
 
 The source code for the libraries, programs, or packages that we use is
 available on our web site at

diff --git a/M2/Macaulay2/d/CMakeLists.txt b/M2/Macaulay2/d/CMakeLists.txt
@@ -45,6 +45,7 @@ set(DLIST
   pthread0.d
   stdiop0.d
   gmp.d
+  ballarith.d
   engine.dd
   xml.d		# removed unless WITH_XML
   stdio0.d

diff --git a/M2/Macaulay2/d/Makefile.files.in b/M2/Macaulay2/d/Makefile.files.in
@@ -34,6 +34,7 @@ M2_DFILES += interrupts.d
 M2_DFILES += pthread0.d
 M2_DFILES += stdiop0.d 
 M2_DFILES += gmp.d
+M2_DFILES += ballarith.d
 M2_DFILES += engine.dd
 ifeq (@XML@,yes)
 M2_DFILES += xml.d