Merge branch 'pre-master'

Macaulay2 · Jan 17, 2021 · ebafe09 · ebafe09
2 parents 2cabd6b + 47eabeb
commit ebafe09
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diff --git a/.github/workflows/test_build.yml b/.github/workflows/test_build.yml
@@ -32,7 +32,7 @@ jobs:
     name: ${{ matrix.build-system }}-${{ matrix.os }}-${{ matrix.compiler }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false  # eventually make this true
+      fail-fast: true
       matrix:
         build-system:
           - cmake
@@ -54,11 +54,15 @@ jobs:
             cxx: clang++-10
             cc: clang-10
           # This build tests Clang rather than AppleClang (keep)
-          #- build-system: cmake
-          #  os: macos-latest
-          #  compiler: clang10
-          #  cxx: clang++
-          #  cc: clang
+          - build-system: cmake
+            os: macos-latest
+            compiler: clang10
+            cxx: clang++
+            cc: clang
+        exclude:
+          - build-system: cmake
+            os: macos-latest
+            compiler: default
 
     steps:
       - uses: actions/checkout@v2
@@ -71,9 +75,12 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           brew config
-          # autoconf, libtool are already in the virtual env
-          brew install automake ccache gnu-tar make ninja pkg-config yasm
-          brew install bdw-gc boost cddlib eigen flint glpk libatomic_ops libomp mpfr mpir ncurses ntl tbb
+          brew tap macaulay2/tap
+          brew install autoconf automake bison ccache cmake gnu-tar libtool make ninja pkg-config yasm
+          brew install bdw-gc boost eigen gdbm readline libatomic_ops libxml2 libomp tbb
+          brew install gmp mpfr ntl [email protected] [email protected] mpsolve glpk
+          brew install frobby memtailor mathic mathicgb givaro fflas-ffpack
+          brew install 4ti2 cohomcalg csdp gfan lrs nauty normaliz topcom
 
 # ----------------------
 #   Install missing tools and libraries for Linux
@@ -88,10 +95,9 @@ jobs:
           sudo apt-get install -y -q --no-install-recommends libatomic-ops-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 libntl-dev gfan \
-                  libcdd-dev libgivaro-dev libboost-regex-dev fflas-ffpack w3c-markup-validator \
-                  cohomcalg libflint-dev libmps-dev topcom \
-                  libsingular-dev libfrobby-dev libgtest-dev libmemtailor-dev libmathic-dev \
-                  libmathicgb-dev 4ti2 normaliz coinor-csdp nauty lrslib singular-data
+                  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
 
 # ----------------------
 #   Steps common to all build variants
@@ -101,7 +107,6 @@ jobs:
         run: |
           echo "CC=${{ matrix.cc }}" >> $GITHUB_ENV
           echo "CXX=${{ matrix.cxx }}" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=`brew --prefix`/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
           if [[ "${{ runner.os }}" == "Linux" ]]
           then echo "/usr/lib/ccache" >> $GITHUB_PATH
                # ccache doesn't seem to create the right symlink for clang-10 on ubuntu
@@ -112,17 +117,17 @@ jobs:
           fi
 
       - uses: actions/cache@v2
-        if: matrix.build-system == 'cmake' # TODO: remove when autotools is more efficient with space
+        if: matrix.build-system == 'cmake'
         id: restore-cache
         with:
           path: |
             ~/.ccache
             ~/work/M2/M2/M2/BUILD/build/usr-host
-          key: build-cache-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.build-system }}-${{ hashFiles('**/cmake/*-libraries.cmake') }}
-          restore-keys: |
-            build-cache-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.build-system }}-
-            build-cache-${{ runner.os }}-${{ matrix.compiler }}-
-            build-cache-${{ runner.os }}-
+          key: build-cache-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.build-system }}-${{ hashFiles('**/cmake/*-libraries.cmake', '.github/workflows/test_build.yml') }}
+          # restore-keys: |
+          #   build-cache-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.build-system }}-
+          #   build-cache-${{ runner.os }}-${{ matrix.compiler }}-
+          #   build-cache-${{ runner.os }}-
 
 
 # ----------------------
@@ -132,12 +137,15 @@ jobs:
       - name: Configure Macaulay2 using CMake
         if: matrix.build-system == 'cmake'
         run: |
+          deps=`brew deps --1 --include-optional macaulay2/tap/M2 | tr '\n' ';'`
+          paths=$HOMEBREW_PREFIX/opt/${deps//;/;$HOMEBREW_PREFIX/opt/}
           cmake -S../.. -B. -GNinja \
-            -DCMAKE_BUILD_TYPE=MinSizeRel -DCMAKE_SYSTEM_PREFIX_PATH=`brew --prefix` \
-            -DBUILD_NATIVE=OFF -DBUILD_LIBRARIES="Givaro;FFLAS_FFPACK" # TODO: remove when the packages are updated
+            -DCMAKE_BUILD_TYPE=MinSizeRel -DBUILD_NATIVE=OFF \
+            -DCMAKE_PREFIX_PATH=$paths \
+            -DCMAKE_INSTALL_PREFIX=/usr
 
       - name: Build libraries using Ninja
-        if: matrix.build-system == 'cmake' # && steps.restore-cache.outputs.cache-hit != 'true'
+        if: matrix.build-system == 'cmake'
         run: |
           cmake --build . --target build-libraries build-programs
 
@@ -160,6 +168,8 @@ jobs:
         run: |
           make -C ../.. get-libtool get-automake get-autoconf
           make -C ../.. all
+          export CPPFLAGS=-I`brew --prefix`/include
+          export  LDFLAGS=-L`brew --prefix`/lib
           ../../configure --enable-download
 
       - name: Build Macaulay2 using Make
@@ -200,6 +210,7 @@ jobs:
            path: |
              # Autotools
              M2/BUILD/build/config.log
+             M2/BUILD/build/include/*
              M2/BUILD/build/libraries/*/build/*/config.log
              # CMake
              M2/BUILD/build/CMakeFiles/CMakeCache.txt

diff --git a/M2/BUILD/docker/.gitignore b/M2/BUILD/docker/.gitignore
@@ -1,2 +1,3 @@
 storage
 !storage/.emacs
+nightly/*.zip
diff --git a/M2/BUILD/docker/Dockerfile b/M2/BUILD/docker/Dockerfile
@@ -1,20 +1,24 @@
-FROM ubuntu:bionic
+# Time usage: <5min
+# Net usage:  ~200MB
+# Disk usage: <800MB docker image
+
+FROM ubuntu:focal
 
 # Setting up Macaulay2 repository
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends apt-transport-https ca-certificates curl gnupg && \
-    curl https://faculty.math.illinois.edu/Macaulay2/PublicKeys/Macaulay2-key -s --output - | apt-key add - && \
-    echo 'deb http://www.math.uiuc.edu/Macaulay2/Repositories/Ubuntu bionic main' > \
-	/etc/apt/sources.list.d/macaulay2.list && apt-get update && apt-get clean
+    apt-get install -y --no-install-recommends software-properties-common apt-transport-https && \
+    add-apt-repository ppa:profzoom/macaulay2 && add-apt-repository ppa:profzoom/macaulay2 && \
+    apt-get update && apt-get clean
 
 # Install Macaulay2
-RUN apt-get install -y macaulay2 && apt-get clean
+RUN apt-get install -y --no-install-recommends macaulay2 && apt-get clean
 
 # Install optional packages
-RUN apt-get install -y emacs bash-completion git mlocate && apt-get clean && updatedb
+RUN apt-get install -y emacs elpa-macaulay2 bash-completion curl git mlocate && \
+    apt-get clean && updatedb
 
 # Add non-root user for running Macaulay2
-RUN useradd -G sudo -g root -u 1000 -m macaulay
+RUN useradd -G sudo -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 USER 1000:0
 
 # Setting environment variables

diff --git a/M2/BUILD/docker/Makefile b/M2/BUILD/docker/Makefile
@@ -1,18 +1,18 @@
 ## Parameters
 TAG = m2
-STORAGE = `pwd`/storage
-M2_REPO = `pwd`/../../..
 M2_HOME = /home/macaulay
+M2_REPO = $(shell git rev-parse --show-toplevel)
+STORAGE = $(M2_REPO)/M2/BUILD/docker/storage
 VOLUME = --volume $(STORAGE):$(M2_HOME) --volume $(M2_REPO):$(M2_HOME)/M2
-BUILD_DIR = M2/M2/BUILD/build-docker
+BUILD_DIR = M2/BUILD/build-docker
 
 ###############################################################################
 
 always:; @cat README.md
 
 all: build run
 
-clean:;	rm -rf ${M2_REPO}/../$(BUILD_DIR) $(STORAGE)/.ccache
+clean:; [[ "$(BUILD_DIR)" =~ "M2/BUILD/build".* ]] && rm -rf $(M2_REPO)/$(BUILD_DIR) $(STORAGE)/.ccache
 
 ###############################################################################
 # Build targets
@@ -25,18 +25,19 @@ build-image:;	docker build --tag $(TAG) .
 # M2 targets
 
 run: run-emacs
+run-M2:;	docker run $(VOLUME) -it --entrypoint M2 $(TAG)
+run-M2-safe:;	docker run $(VOLUME) -it --entrypoint M2 $(TAG) -q --int --no-readline --no-randomize --no-threads
+run-emacs-tui:;	docker run $(VOLUME) -it --entrypoint emacs $(TAG)
+run-emacs:;	docker run $(VOLUME) --entrypoint emacs --net=host --env="DISPLAY" $(TAG)
 
-run-M2:;	docker run $(VOLUME) -it --entrypoint="" $(TAG) M2
-
-run-M2-safe:;	docker run $(VOLUME) -it --entrypoint="" $(TAG) M2 -q --int --no-readline --no-randomize --no-threads
-
-run-emacs-tui:;	docker run $(VOLUME) -it $(TAG)
-
-run-emacs:;	docker run $(VOLUME) --net=host --env="DISPLAY" $(TAG)
+check: check-1
+check-1:;	docker run $(VOLUME) -it --entrypoint M2 $(TAG) -q --no-preload --check 1 -e 'exit 0'
+check-2:;	docker run $(VOLUME) -it --entrypoint M2 $(TAG) -q --no-preload --check 2 -e 'exit 0'
+check-3:;	docker run $(VOLUME) -it --entrypoint M2 $(TAG) -q --no-preload --check 3 -e 'exit 0'
 
 ###############################################################################
 # Terminal targets
 
-root:;	docker run $(VOLUME) -it -w $(M2_HOME)/$(BUILD_DIR) --user root --entrypoint bash $(TAG)
+root:;	docker run $(VOLUME) -it -w $(M2_HOME)/M2/$(BUILD_DIR) --user root --entrypoint bash $(TAG)
 
-shell:;	docker run $(VOLUME) -it -w $(M2_HOME)/$(BUILD_DIR) --entrypoint bash $(TAG)
+shell:;	docker run $(VOLUME) -it -w $(M2_HOME)/M2/$(BUILD_DIR) --entrypoint bash $(TAG)
diff --git a/M2/BUILD/docker/README.md b/M2/BUILD/docker/README.md
@@ -2,11 +2,13 @@
 
 Docker is a containerization program for building, shipping, or running applications on different platforms.
 
-The `Dockerfile` in this directory creates a container image based on Ubuntu 18.04.4 with Macaulay2 installed from the repository. Each subdirectory contains a `Dockerfile` built for other use cases:
+The `Dockerfile` in this directory creates a container image based on Ubuntu 20.04.1 LTS with Macaulay2 installed from the repository. Each subdirectory contains a `Dockerfile` built for other use cases:
 
-- `ubuntu`: Compiling Macaulay2 in a Container
-- `debian`: Packaging Macaulay2 for Debian (.deb)
-- `fedora`: Packaging Macaulay2 for Fedora (.rpm)
+- [`ubuntu`](ubuntu):   Compiling Macaulay2 in a Container
+- [`debian`](debian):   Packaging Macaulay2 for Debian (.deb)
+- [`fedora`](fedora):   Packaging Macaulay2 for Fedora (.rpm)
+- [`brew`](brew):       Bottling  Macaulay2 for [Homebrew](https://brew.sh/)
+- [`nightly`](nightly): Testing the Nightly Build of Macaulay2
 
 ## Getting Started
 0. Install Docker and start the daemon.

diff --git a/M2/BUILD/docker/brew/Dockerfile b/M2/BUILD/docker/brew/Dockerfile
@@ -0,0 +1,27 @@
+# Time usage: <15min
+# Net usage:  ~700MB
+# Disk usage: ~1GB
+
+FROM linuxbrew/brew
+
+# Install optional packages
+RUN apt-get update && apt-get install -y -q --no-install-recommends vim mlocate && apt-get clean
+
+USER 1000:0
+
+# Add the tap containing the formulae for Macaulay2 and its dependencies
+RUN brew update && brew config && brew tap Macaulay2/tap
+
+RUN brew install bash-completion && echo '\n\
+    [[ -r "`brew --prefix`/etc/profile.d/bash_completion.sh" ]] && \n\
+	. "`brew --prefix`/etc/profile.d/bash_completion.sh"' >> /home/linuxbrew/.bashrc
+
+# Install dependencies of Macaulay2
+#RUN brew install --only-dependencies Macaulay2/tap/macaulay2
+
+# Install Macaulay2
+#RUN brew install --verbose --build-bottle Macaulay2/tap/macaulay2
+
+RUN sudo updatedb
+
+WORKDIR /home/linuxbrew
diff --git a/M2/BUILD/docker/brew/Makefile b/M2/BUILD/docker/brew/Makefile
@@ -0,0 +1,35 @@
+## Parameters
+TAG = m2-homebrew
+M2_HOME = /home/linuxbrew
+M2_REPO = $(shell git rev-parse --show-toplevel)
+STORAGE = $(M2_REPO)/M2/BUILD/docker/storage
+
+VOLUME-A = --volume /home/linuxbrew:$(M2_HOME)
+VOLUME-B = --volume $(STORAGE)/.cache:$(M2_HOME)/.cache
+VOLUME-C = --volume $(M2_REPO):$(M2_HOME)/M2
+
+###############################################################################
+
+always:; @cat README.md
+
+all: build shell
+
+###############################################################################
+# Build targets
+
+build: build-image
+
+build-image:; docker build --tag $(TAG) .
+
+###############################################################################
+# Terminal targets
+
+shell: shell-linux
+
+# Run this on Linux
+shell-linux:; docker run $(VOLUME-A) $(VOLUME-C) -it --entrypoint bash $(TAG)
+
+# Run this on macOS
+shell-macos:; docker run $(VOLUME-B) $(VOLUME-C) -it --entrypoint bash $(TAG)
+
+shell-raw:;   docker run $(VOLUME-C) -it --entrypoint bash $(TAG)
diff --git a/M2/BUILD/docker/brew/README.md b/M2/BUILD/docker/brew/README.md
@@ -0,0 +1,22 @@
+# Bottling Macaulay2 for [Homebrew](https://brew.sh/)
+
+Homebrew is a package manager for macOS and Linux. The `Dockerfile` in this directory creates a container image based on Ubuntu 20.04 for building and testing the Homebrew formula for Macaulay2 available at [`Macaulay2/tap`](https://github.com/Macaulay2/homebrew-tap).
+
+## Getting Started
+0. Install Docker and start the daemon (optionally, also install [Homebrew](https://brew.sh/)).
+
+1. Build the container using Docker:
+```
+make build
+```
+
+2. Enter the shell:
+```
+make shell-linux # if you are using Linuxbrew
+make shell-macos # if you are using Homebrew
+```
+
+3. Bottle Macaulay2:
+```
+brew install --keep-tmp --verbose --build-bottle Macaulay2/tap/M2
+```
diff --git a/M2/BUILD/docker/debian/Dockerfile b/M2/BUILD/docker/debian/Dockerfile
@@ -30,7 +30,7 @@ RUN apt-get install -y libeigen3-dev  libglpk-dev libgmp3-dev libmpfr-dev \
 RUN apt-get install -y mlocate bash-completion
 
 # Add non-root user for building and running Macaulay2
-RUN useradd -G sudo -g root -u 1000 -m macaulay
+RUN useradd -G sudo -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 USER 1000:0
 
 ENV PKG_CONFIG_PATH /usr/lib/x86_64-linux-gnu/pkgconfig

diff --git a/M2/BUILD/docker/debian/Makefile b/M2/BUILD/docker/debian/Makefile
@@ -2,12 +2,8 @@ include ../ubuntu/Makefile
 
 ## Parameters
 TAG = m2-debian-build
-STORAGE = `pwd`/../storage
-M2_REPO = `pwd`/../../../..
-M2_HOME = /home/macaulay
-VOLUME = --volume $(STORAGE):$(M2_HOME) --volume $(M2_REPO):$(M2_HOME)/M2
-BUILD_DIR = M2/M2/BUILD/build-docker
-BUILD_OPT = -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DUSING_MPIR=OFF
+BUILD_DIR = M2/BUILD/build-docker
+BUILD_OPT = -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr
 
 deb:;       docker run $(VOLUME) -it --entrypoint "" $(TAG) bash -c "cd $(BUILD_DIR); cpack -G DEB"
 

diff --git a/M2/BUILD/docker/fedora/Dockerfile b/M2/BUILD/docker/fedora/Dockerfile
@@ -24,7 +24,7 @@ RUN microdnf install eigen3-devel glpk-devel gmp-devel mpfr-devel ntl-devel libf
 RUN microdnf install mlocate bash-completion
 
 # Add non-root user for building and running Macaulay2
-RUN useradd -G wheel -g root -u 1000 -m macaulay
+RUN useradd -G wheel -g root -u 1000 -m macaulay && echo "macaulay ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
 USER 1000:0
 
 ENV PATH /home/macaulay/M2/M2/BUILD/build-docker:${PATH}

diff --git a/M2/BUILD/docker/fedora/Makefile b/M2/BUILD/docker/fedora/Makefile
@@ -2,12 +2,8 @@ include ../ubuntu/Makefile
 
 ## Parameters
 TAG = m2-fedora-build
-STORAGE = `pwd`/../storage
-M2_REPO = `pwd`/../../../..
-M2_HOME = /home/macaulay
-VOLUME = --volume $(STORAGE):$(M2_HOME) --volume $(M2_REPO):$(M2_HOME)/M2
-BUILD_DIR = M2/M2/BUILD/build-docker
-BUILD_OPT = -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DUSING_MPIR=OFF
+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 $(BUILD_DIR); cpack -G RPM"