Hilbert schemes

.codespell_ignore

@@ -0,0 +1,73 @@
+afterwords
+alledges
+allready
+alot
+alph
+ans
+anumber
+archiv
+assasin
+ba
+bloks
+braket
+bu
+comon
+coo
+damon
+debugg
+dorder
+egal
+enew
+euclidian
+exitance
+falsy
+falt
+firsth
+fo
+formes
+freee
+froms
+fullfil
+geometrie
+hart
+includee
+independant
+inh
+inot
+inout
+intall
+ist
+ket
+lamda
+lod
+lond
+lsat
+methd
+mor
+multidimension
+nam
+nd
+nin
+numer
+openin
+ore
+ot
+packge
+pres
+pring
+projet
+reseting
+returne
+ser
+singl
+skelton
+sring
+strat
+sur
+te
+thets
+toom
+translater
+tring
+trough
+ue

.github/workflows/lint.yml

@@ -0,0 +1,20 @@
+name: Lint
+on:
+  push: { branches: [ "development" ] }
+  pull_request: { branches: [ "development" ] }
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          sudo apt-get install -y codespell
+      - name: Run codespell
+        shell: bash -l {0}
+        run: codespell --ignore-words=.codespell_ignore M2/Macaulay2/packages
+
+env:
+  MAKEFLAGS: -j2

.github/workflows/test_build.yml

@@ -9,15 +9,14 @@
 name: Build and Test Macaulay2
 
 on:
+  workflow_dispatch:
   push:
     branches:
-      - release-1.17
       - 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
-      - release-1.17
   schedule:
     # cron time in UTC
     # a scheduled job runs on the default branch: 'master'
@@ -33,36 +32,37 @@ jobs:
     name: ${{ matrix.build-system }}-${{ matrix.os }}-${{ matrix.compiler }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false  # eventually make this true
+      fail-fast: false
       matrix:
         build-system:
           - cmake
           - autotools
         os:
-          - ubuntu-latest
-          - macos-latest
+          - ubuntu-22.04
+          - macos-12
         compiler:
-          - gcc9
           - default
         include:
           - build-system: cmake
-            compiler: gcc9
-            cxx: g++-9
-            cc: gcc-9
+            os: ubuntu-22.04
+            compiler: clang-14
+            cxx: clang++-14
+            cc: clang-14
+          # This build tests Clang rather than AppleClang (keep)
           - build-system: cmake
-            os: ubuntu-latest
-            compiler: clang10
-            cxx: clang++-10
-            cc: clang-10
+            os: macos-12
+            compiler: clang-15
+            cxx: clang++
+            cc: clang
         exclude:
-          - build-system: autotools
-            compiler: gcc9
           - build-system: cmake
-            os: macos-latest
-            compiler: gcc9
+            os: macos-12
+            compiler: default
+    env:
+      VERBOSE: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
 # ----------------------
 #   Install missing tools and libraries for macOS
@@ -72,9 +72,9 @@ 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 automake boost tbb ccache ctags llvm@14 make ninja yasm libffi
+          brew install --only-dependencies macaulay2/tap/M2
 
 # ----------------------
 #   Install missing tools and libraries for Linux
@@ -83,44 +83,43 @@ jobs:
       - name: Install requirements for Linux
         if: runner.os == 'Linux'
         run: |
-          sudo add-apt-repository -y ppa:profzoom/macaulay2
+          sudo add-apt-repository -y -n ppa:macaulay2/macaulay2
           sudo apt-get update
-          sudo apt-get install -y -q --no-install-recommends clang-10 gfortran libtool-bin ninja-build yasm ccache
+          sudo apt-get install -y -q --no-install-recommends clang-14 gfortran libtool-bin ninja-build yasm ccache
           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
+                  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-14-dev
 
 # ----------------------
 #   Steps common to all build variants
 # ----------------------
 
       - name: Prepare build environment
         run: |
-          echo "CC=${{ matrix.cc }}" >> $GITHUB_ENV
+          echo "CC=${{  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
+          then alias llvm-config="llvm-config-14"
+               echo "/usr/lib/ccache"                     >> $GITHUB_PATH
           else echo `brew --prefix ccache`/libexec        >> $GITHUB_PATH
                echo `brew --prefix make  `/libexec/gnubin >> $GITHUB_PATH
+               echo `brew --prefix llvm@14`/bin              >> $GITHUB_PATH
+               PATH=`brew --prefix llvm@14`/bin:$PATH
           fi
+          # Necessary for clang to find the right libomp
+          echo "LIBRARY_PATH=`llvm-config --libdir`" >> $GITHUB_ENV
 
-      - uses: actions/cache@v2
-        if: matrix.build-system == 'cmake' # TODO: remove when autotools is more efficient with space
+      - uses: actions/cache@v3
+        if: matrix.build-system == 'cmake'
         id: restore-cache
         with:
           path: |
             ~/.ccache
-            ~/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 }}-
+            ~/work/M2/M2/M2/BUILD/build/usr-host
+          key: build-cache-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.build-system }}-${{ hashFiles('**/cmake/*-libraries.cmake', '.github/workflows/test_build.yml') }}
 
 
 # ----------------------
@@ -131,18 +130,26 @@ jobs:
         if: matrix.build-system == 'cmake'
         run: |
           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=Release -DBUILD_NATIVE=OFF \
+            -DCMAKE_PREFIX_PATH="`brew --prefix`;`brew --prefix libffi`" \
+            -DCMAKE_INSTALL_PREFIX=/usr \
+            -DWITH_PYTHON=ON \
+            --debug-trycompile
 
       - 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
 
       - name: Build Macaulay2 using Ninja
         if: matrix.build-system == 'cmake'
         run: |
-          cmake --build . --target M2-core install-packages
+          cmake --build . --target M2-core M2-emacs install-packages
+          if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.compiler }}" == "clang-14" ]]; 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
+          fi
 
 # ----------------------
 #   Configure and build M2 using Autotools
@@ -153,7 +160,12 @@ jobs:
         run: |
           make -C ../.. get-libtool get-automake get-autoconf
           make -C ../.. all
-          ../../configure --enable-download
+          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"
+          ../../configure --enable-download --with-python --with-system-gc
 
       - name: Build Macaulay2 using Make
         if: matrix.build-system == 'autotools'
@@ -165,37 +177,78 @@ jobs:
 # ----------------------
 
       - name: Run Tests using CTest
-        if: matrix.build-system == 'cmake' && matrix.compiler == 'default'
+        if: matrix.build-system == 'cmake' && runner.os == 'Linux' && matrix.compiler == 'clang-14'
         run: |
-          # cmake --build . --target M2-unit-tests
-          # ctest -R "unit-tests"
-          # TODO: remove the excluded normal tests
-          ctest -R "normal/" -E "command|program|schenck|threads|doc-links" -j4 --output-on-failure
-          # TODO: add engine tests
+          set -xe
+          ./M2 -q --check 1 -e 'exit 0'
+          ./M2 -q --check 2 -e 'exit 0'
+          ./M2 -q --check 3 -e 'exit 0'
+          cmake --build . --target M2-tests
+          cmake --build . --target M2-unit-tests
+          cmake --build . --target memtailor-unit-tests mathic-unit-tests mathicgb-unit-tests
+          ctest -j1 --output-on-failure -R "unit-tests"
+          ctest -j4 --output-on-failure -R "ComputationsBook"
+          # TODO: add Macaulay2/tests/engine when https://github.com/Macaulay2/M2/issues/1213 is fixed
 
       - name: Run Tests using Autotools
-        if: matrix.build-system == 'autotools' && matrix.os == 'ubuntu-latest' && matrix.compiler == 'default'
+        if: matrix.build-system == 'autotools' && runner.os == 'Linux' && matrix.compiler == 'default'
         run: |
           make check -o check-in-libraries
           make -C Macaulay2/html-check-links check
-          make validate-html
+
+      - name: Validate HTML documentation
+        if: matrix.build-system == 'autotools' && runner.os == 'Linux'
+        run: |
+          python3 -m pip install html5validator
+          if test ${{ github.event_name }} = pull_request
+          then
+            git fetch --depth=1 origin development
+            # validate everything if any changes to Core
+            if test "$(git diff --stat origin/development HEAD -- ../../Macaulay2/m2)"
+            then
+              make validate-html
+            else
+            # otherwise, just validate HTML docs for packages that have been updated
+              PACKAGES=$(git diff --stat origin/development HEAD -- ../../Macaulay2/packages/ | grep -Po "(?<=Macaulay2/packages/)[^/\.]*(?=\.m2|/)" | uniq)
+              make validate-html PACKAGES="$PACKAGES"
+            fi
+          else
+            # if not a pull request (scheduled or pre-master builds), then validate everything
+            make validate-html
+          fi
 
 # ----------------------
-#   Upload build logs
+#   Upload build artifacts
 # ----------------------
 
       - name: Upload build logs
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
            name: ${{ matrix.build-system }}-${{ matrix.os }}-${{ matrix.compiler }}-logs
            path: |
              # Autotools
              M2/BUILD/build/config.log
+             M2/BUILD/build/include/*
              M2/BUILD/build/libraries/*/build/*/config.log
              # CMake
-             M2/BUILD/build/CMakeFiles/CMakeCache.txt
-             M2/BUILD/build/CMakeFiles/CMake(Error|Output).log
+             M2/BUILD/build/CMakeCache.txt
+             M2/BUILD/build/CMakeFiles/CMakeError.log
+             M2/BUILD/build/CMakeFiles/CMakeOutput.log
              M2/BUILD/build/libraries/*/build/config.log
-             # Example errors
+             # package example errors
              M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/*/example-output/*.errors
+             # package test errors under Ubuntu
+             /tmp/M2-*/*.tmp
+             /tmp/M2-*/*.m2
+             # Test errors
+             M2/BUILD/build/Macaulay2/tests/*/*.errors
+
+      - name: Upload Macaulay2 package for Ubuntu (x86_64)
+        if: matrix.build-system == 'cmake' && runner.os == 'Linux' && matrix.compiler == 'clang-14' && success()
+        uses: actions/upload-artifact@v3
+        with:
+          name: Macaulay2-${{ env.GIT_COMMIT }}-ubuntu-x86_64
+          path: |
+            M2/BUILD/build/Macaulay2-*
+          retention-days: 1

.gitignore

@@ -2,13 +2,15 @@
 /M2/Macaulay2/m2/TAGS.doc
 /M2/build-vscode
 /M2/BUILD/dan/builds.tmp
+/M2/BUILD/frank
 /M2/autom4te.cache
 /M2/configure
 /M2/include/M2/config.h.in
 /M2/include/M2/config.h.in~
 /M2/include/M2/config.h
 /M2/include/M2/config.h.in.stamp
 /M2/.idea
+/M2/tmp
 /builds
 .DS_Store
 .#*