MatchingPowers - A Macaulay2 package for computing the matching powers of monomial ideals

.codespell_ignore

@@ -1,8 +1,5 @@
-afterwords
 alledges
 allready
-alot
-alph
 ans
 anumber
 archiv
@@ -14,9 +11,8 @@ bu
 comon
 conet
 coo
-damon
-debugg
 dorder
+debugg
 egal
 enew
 euclidian
@@ -28,18 +24,15 @@ fo
 formes
 freee
 froms
-fullfil
 geometrie
 hart
 includee
-independant
 inh
 inot
 inout
 intall
 ist
 ket
-lamda
 lod
 lond
 lsat
@@ -57,18 +50,13 @@ packge
 pres
 pring
 projet
-reseting
-returne
 ser
-singl
 skelton
 sring
+sring
 strat
 sur
 te
-thets
 toom
-translater
 tring
-trough
 ue

.github/dependabot.yml

@@ -0,0 +1,37 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-action-dependencies:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "npm"
+    directory: "/M2/Macaulay2/editors/prism"
+    schedule:
+      interval: "monthly"
+    groups:
+      prism-dependencies:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "npm"
+    directory: "/M2/Macaulay2/packages/Style"
+    schedule:
+      interval: "monthly"
+    groups:
+      style-dependencies:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "npm"
+    directory: "/M2/Macaulay2/packages/Visualize"
+    schedule:
+      interval: "monthly"
+    groups:
+      visualize-dependencies:
+        patterns:
+          - "*"

.github/pull_request_template.md

@@ -0,0 +1,5 @@
+<!--
+Thank you for contributing to Macaulay2!
+
+Please read https://github.com/Macaulay2/M2/wiki/Pull-requests for instructions.
+-->

.github/workflows/lint.yml

@@ -1,7 +1,5 @@
 name: Lint
-on:
-  push: { branches: [ "development" ] }
-  pull_request: { branches: [ "development", "master" ] }
+on: [ push, pull_request ]
 
 jobs:
   codespell:

.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
@@ -82,13 +79,13 @@ jobs:
         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 normaliz coinor-csdp \
-                  nauty lrslib polymake phcpack w3c-markup-validator libtbb-dev qepcad libomp-15-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
 
 # ----------------------
 #   Steps common to all build variants
@@ -100,7 +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        >> $GITHUB_PATH
@@ -145,7 +142,7 @@ jobs:
         if: matrix.build-system == 'cmake'
         run: |
           cmake --build . --target M2-core M2-emacs install-packages
-          if [[ "${{ 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
@@ -176,7 +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'
@@ -198,7 +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
@@ -244,7 +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

.gitmodules

@@ -10,12 +10,6 @@
 [submodule "M2/submodules/bdwgc"]
 	path = M2/submodules/bdwgc
 	url = https://github.com/Macaulay2/bdwgc.git
-[submodule "M2/submodules/libatomic_ops"]
-	path = M2/submodules/libatomic_ops
-	url = https://github.com/Macaulay2/libatomic_ops.git
-[submodule "M2/submodules/mpir"]
-	path = M2/submodules/mpir
-	url = https://github.com/Macaulay2/mpir.git
 [submodule "M2/submodules/flint"]
 	path = M2/submodules/flint
 	url = https://github.com/Macaulay2/flint2.git
@@ -27,7 +21,7 @@
 	url = https://github.com/Macaulay2/fflas-ffpack.git
 [submodule "M2/submodules/givaro"]
 	path = M2/submodules/givaro
-	url = https://github.com/Macaulay2/givaro.git
+	url = https://github.com/linbox-team/givaro
 [submodule "M2/submodules/googletest"]
 	path = M2/submodules/googletest
 	url = https://github.com/google/googletest.git

M2/BUILD/dan/README

@@ -5,7 +5,7 @@ Solaris
 
 Ubuntu 12 hint:
 
-    I was working on Ubuntu 12.04, but I had to upgrade on Ubuntu 11.10, and, after some difficulties I find a solution to intall correctly M2 :
+    I was working on Ubuntu 12.04, but I had to upgrade on Ubuntu 11.10, and, after some difficulties I find a solution to install correctly M2 :
     1) I first get the  "libpari2-gmp" debian package at http://security.ubuntu.com/ubuntu/pool/universe/p/pari/
     2) I install the  "libgmp3c2" package with an apt-get install
     3) I do a dpkg on the "libpari2-gmp" package

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 \
-	libsingular-dev singular-data libmemtailor-dev libmathic-dev libmathicgb-dev libcdd-dev \
-	cohomcalg topcom 4ti2 normaliz coinor-csdp nauty lrslib w3c-markup-validator libtbb-dev
+	libnauty-dev libnormaliz-dev libsingular-dev singular-data libcdd-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

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

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

M2/BUILD/docker/debian/Dockerfile

@@ -16,12 +16,9 @@ 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 libfrobby-dev libgc-dev && apt-get clean
+      libntl-dev libnauty-dev libnormaliz-dev libfrobby-dev libgc-dev && apt-get clean
 
 # Programs we can build
 # TODO: cohomcalg available soon. Polymake requires firefox???

M2/BUILD/docker/fedora/Dockerfile

@@ -11,10 +11,11 @@ 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 libfrobby-devel gc-devel
+RUN microdnf install eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel \
+	libnauty-devel libnormaliz-devel libfrobby-devel gc-devel
 
 # Programs we can build
 # TODO: cohomcalg available soon. Polymake requires firefox???

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