Merge remote-tracking branch 'upstream/development' into Permutations

Author: seangrate

.github/workflows/test_build.yml

@@ -66,7 +66,7 @@ jobs:
           brew config
           brew tap macaulay2/tap
           brew install --overwrite python
-          brew install automake boost tbb ccache ctags texinfo llvm make ninja yasm libffi msolve
+          brew install automake boost tbb ccache ctags texinfo llvm make ninja yasm libffi msolve googletest
           brew install --only-dependencies macaulay2/tap/M2
           brew link factory --force
 
@@ -155,11 +155,12 @@ jobs:
         if: matrix.build-system == 'autotools'
         run: |
           ../../autogen.sh
-          export PYVERSION=`python3 -c "from sys import version_info; \
-            print(f'{version_info.major}.{version_info.minor}')"`
-          export CPPFLAGS="-I`brew --prefix`/include -I`brew --prefix libomp`/include"
-          export  LDFLAGS="-L`brew --prefix`/lib -L`brew --prefix libomp`/lib \
-            -L/Library/Frameworks/Python.framework/Versions/${PYVERSION}/lib"
+          export CPPFLAGS="-I`brew --prefix`/include \
+            -I`brew --prefix libomp`/include         \
+            -I`brew --prefix readline`/include"
+          export  LDFLAGS="-L`brew --prefix`/lib \
+            -L`brew --prefix libomp`/lib         \
+            -L`brew --prefix readline`/lib"
           export F77=gfortran-14
           ../../configure --enable-download --with-system-gc
 
@@ -205,7 +206,7 @@ jobs:
               make validate-html
             else
             # otherwise, just validate HTML docs for packages that have been updated
-              PACKAGES=$(git diff --stat origin/development HEAD -- ../../Macaulay2/packages/ | grep -Po "(?<=Macaulay2/packages/)[^/\.]*(?=\.m2|/)" | uniq | xargs)
+              PACKAGES=$(git diff --stat origin/development HEAD -- ../../Macaulay2/packages/ | grep -Po "(?<=Macaulay2/packages/)[^/\.]*(?=\.m2|/)" | uniq | sed 's/undistributed-packages//g' | xargs)
               make validate-html PACKAGES="$PACKAGES"
             fi
           else

.gitmodules

@@ -1,30 +1,40 @@
 [submodule "M2/submodules/memtailor"]
 	path = M2/submodules/memtailor
 	url = https://github.com/Macaulay2/memtailor
+	ignore = all
 [submodule "M2/submodules/mathic"]
 	path = M2/submodules/mathic
 	url = https://github.com/Macaulay2/mathic
+	ignore = all
 [submodule "M2/submodules/mathicgb"]
 	path = M2/submodules/mathicgb
 	url = https://github.com/Macaulay2/mathicgb
+	ignore = all
 [submodule "M2/submodules/bdwgc"]
 	path = M2/submodules/bdwgc
 	url = https://github.com/Macaulay2/bdwgc.git
+	ignore = all
 [submodule "M2/submodules/flint"]
 	path = M2/submodules/flint
-	url = https://github.com/Macaulay2/flint2.git
+	url = https://github.com/flintlib/flint
+	ignore = all
 [submodule "M2/submodules/frobby"]
 	path = M2/submodules/frobby
 	url = https://github.com/Macaulay2/frobby.git
+	ignore = all
 [submodule "M2/submodules/fflas-ffpack"]
 	path = M2/submodules/fflas_ffpack
 	url = https://github.com/Macaulay2/fflas-ffpack.git
+	ignore = all
 [submodule "M2/submodules/givaro"]
 	path = M2/submodules/givaro
 	url = https://github.com/linbox-team/givaro
+	ignore = all
 [submodule "M2/submodules/googletest"]
 	path = M2/submodules/googletest
 	url = https://github.com/google/googletest.git
+	ignore = all
 [submodule "M2/Macaulay2/editors/emacs"]
 	path = M2/Macaulay2/editors/emacs
 	url = https://github.com/Macaulay2/M2-emacs.git
+	ignore = all

M2/BUILD/docker/fedora/Dockerfile

@@ -2,27 +2,33 @@
 # Net usage:  54+124+
 # Disk usage: ??
 
-FROM registry.fedoraproject.org/fedora-minimal:32
+ARG RELEASE=latest
+
+FROM quay.io/fedora/fedora-minimal:$RELEASE
 
 # Programs we require to build
 #  kernel-devel rpm-build rpm-sign rpmdevtools
-RUN microdnf install autoconf bison ccache cmake curl diffutils file gcc-c++ git \
-	gnupg libtool make ninja-build patch yasm rpm-build rpmlint which
+RUN microdnf install -y autoconf bison ccache cmake curl diffutils file     \
+    gcc-c++ git gnupg libtool make ninja-build patch yasm rpm-build rpmlint \
+    which flex gcc-gfortran
 
 # Libraries we require
-RUN microdnf install openblas-devel libxml2-devel readline-devel gdbm-devel \
-	boost-devel libomp-dev libtbb-dev
+RUN microdnf install -y openblas-devel libxml2-devel readline-devel gdbm-devel \
+    boost-devel libomp-devel tbb-devel python3-devel libffi-devel
 
 # Libraries we can build (factory not available on ubuntu)
-RUN microdnf install eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel \
-	libnauty-devel libnormaliz-devel libfrobby-devel gc-devel
+RUN microdnf install -y eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel \
+    libnauty-devel libnormaliz-devel libfrobby-devel gc-devel mpfi-devel       \
+    factory-devel mpsolve-devel fflas-ffpack-devel memtailor-devel             \
+    mathic-devel mathicgb-devel
 
 # Programs we can build
-# TODO: cohomcalg available soon. Polymake requires firefox???
-#RUN microdnf install libcdd-devel 4ti2 gfan normaliz coinor-csdp nauty lrslib
+# TODO: Polymake requires firefox???
+RUN microdnf install -y cddlib-devel 4ti2 gfan normaliz csdp-tools nauty \
+    lrslib-utils cohomCalg msolve
 
 # Optional packages
-RUN microdnf install mlocate bash-completion
+RUN microdnf install -y plocate bash-completion R
 
 # Add non-root user for building and running Macaulay2
 RUN useradd -G wheel -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers

M2/BUILD/docker/fedora/Makefile

@@ -1,10 +1,33 @@
 include ../ubuntu/Makefile
 
 ## Parameters
-TAG = m2-fedora-build
+RELEASE = latest
+BUILD_ARGS = --build-arg RELEASE=$(RELEASE)
+TAG = m2-fedora-$(RELEASE)-build
 BUILD_DIR = M2/BUILD/build-docker
 BUILD_OPT = -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr
 
 rpm:;       docker run $(VOLUME) -it --entrypoint "" $(TAG) bash -c "cd M2/$(BUILD_DIR); cpack -G RPM"
 
 rpmlint:;   docker run $(VOLUME) -it --entrypoint "" $(TAG) bash -c "rpmlint M2/$(BUILD_DIR)/Macaulay2-*.rpm"
+
+## autotools build
+## TODO: generalize this to other distros, move to toplevel Makefile
+
+CONFIG_OPT = --with-system-gc --with-system-memtailor --with-system-mathic \
+	--with-system-mathicgb --enable-download --enable-rpm --prefix=/usr
+
+define M2_BUILD_SCRIPT_autotools
+set -xe
+
+mkdir -p M2/$(BUILD_DIR)
+cd M2/$(BUILD_DIR)
+$(M2_HOME)/M2/M2/autogen.sh
+$(M2_HOME)/M2/M2/configure $(CONFIG_OPT)
+make
+endef
+export M2_BUILD_SCRIPT_autotools
+
+build-autotools: build-image
+	docker run $(VOLUME) -it --entrypoint="" $(TAG) \
+		bash -c "$$M2_BUILD_SCRIPT_autotools"

M2/BUILD/docker/testbot/Dockerfile

@@ -1,14 +1,16 @@
 # Time usage: <5min
 # Net usage:  <200MB
-# Disk usage: <700MB
+# Disk usage: <800MB
 
 FROM debian:bookworm
 
+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
 
 # 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 && apt-get clean
+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
 
 # 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

M2/BUILD/docker/testbot/README.md

@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - name: Checkout the project repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Run testbot on project branch
         run: |

M2/CMakeLists.txt

@@ -58,7 +58,7 @@ file(STRINGS VERSION VERSION)
 project(Macaulay2
   VERSION	${VERSION}
   DESCRIPTION	"A software system for algebraic geometry research"
-  HOMEPAGE_URL	http://macaulay2.com # contact: [email protected]
+  HOMEPAGE_URL	https://macaulay2.com # contact: [email protected]
   LANGUAGES	C CXX)
 
 ###############################################################################

M2/LICENSING-NOTES

@@ -9,8 +9,7 @@
 ###############################################################################
 ## Some miscellaneous instructions
 
-# Generate README and copy the copyright license in usr-dist
-configure_file(README.in ${M2_DIST_PREFIX}/${M2_INSTALL_DOCDIR}/README @ONLY)
+# Copy the copyright license in usr-dist
 file(COPY LAYOUT COPYING-GPL-2 COPYING-GPL-3 DESTINATION ${M2_DIST_PREFIX}/${M2_INSTALL_DOCDIR})
 
 # eg: Style Macaulay2Doc ...

M2/Macaulay2/CMakeLists.txt

@@ -2,7 +2,7 @@
 # we want to ignore the --datarootdir setting, whatever that means, so here we we mention it: @datarootdir@
 VPATH = @srcdir@
 include ../include/config.Makefile
-all: @pre_docdir@/COPYING-GPL-2 @pre_docdir@/COPYING-GPL-3 @pre_docdir@/README @pre_docdir@/LAYOUT
+all: @pre_docdir@/COPYING-GPL-2 @pre_docdir@/COPYING-GPL-3 @pre_docdir@/LAYOUT
 SUBDIRS = util c d e system bin m2 man packages editors \
 	$(if $(filter html, @DOCUMENTATION@), html-check-links) tests